[BUGFIX] In-memory columnar storage bug fixes

Fixed several bugs of in-memory columnar storage to make `HiveInMemoryCompatibilitySuite` pass.

@rxin @marmbrus It is reasonable to include `HiveInMemoryCompatibilitySuite` in this PR, but I didn't, since it significantly increases test execution time. What do you think?

**UPDATE** `HiveCompatibilitySuite` has been made to cache tables in memory. `HiveInMemoryCompatibilitySuite` was removed.

Author: Cheng Lian <lian.cs.zju@gmail.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #374 from liancheng/inMemBugFix and squashes the following commits:

6ad6d9b [Cheng Lian] Merged HiveCompatibilitySuite and HiveInMemoryCompatibilitySuite
5bdbfe7 [Cheng Lian] Revert 882c538 & 8426ddc, which introduced regression
882c538 [Cheng Lian] Remove attributes field from InMemoryColumnarTableScan
32cc9ce [Cheng Lian] Code style cleanup
99382bf [Cheng Lian] Enable compression by default
4390bcc [Cheng Lian] Report error for any Throwable in HiveComparisonTest
d1df4fd [Michael Armbrust] Remove test tables that might always get created anyway?
ab9e807 [Michael Armbrust] Fix the logged console version of failed test cases to use the new syntax.
1965123 [Michael Armbrust] Don't use coalesce for gathering all data to a single partition, as it does not work correctly with mutable rows.
e36cdd0 [Michael Armbrust] Spelling.
2d0e168 [Michael Armbrust] Run Hive tests in-memory too.
6360723 [Cheng Lian] Made PreInsertionCasts support SparkLogicalPlan and InMemoryColumnarTableScan
c9b0f6f [Cheng Lian] Let InsertIntoTable support InMemoryColumnarTableScan
9c8fc40 [Cheng Lian] Disable compression by default
e619995 [Cheng Lian] Bug fix: incorrect byte order in CompressionScheme.columnHeaderSize
8426ddc [Cheng Lian] Bug fix: InMemoryColumnarTableScan should cache columns specified by the attributes argument
036cd09 [Cheng Lian] Clean up unused imports
44591a5 [Cheng Lian] Bug fix: NullableColumnAccessor.hasNext must take nulls into account
052bf41 [Cheng Lian] Bug fix: should only gather compressibility info for non-null values
95b3301 [Cheng Lian] Fixed bugs in IntegralDelta
HOTFIX: Use file name and not paths for excludes
SPARK-1488. Resolve scalac feature warnings during build

For your consideration: scalac currently notes a number of feature warnings during compilation:

```
[warn] there were 65 feature warning(s); re-run with -feature for details
```

Warnings are like:

```
[warn] /Users/srowen/Documents/spark/core/src/main/scala/org/apache/spark/SparkContext.scala:1261: implicit conversion method rddToPairRDDFunctions should be enabled
[warn] by making the implicit value scala.language.implicitConversions visible.
[warn] This can be achieved by adding the import clause 'import scala.language.implicitConversions'
[warn] or by setting the compiler option -language:implicitConversions.
[warn] See the Scala docs for value scala.language.implicitConversions for a discussion
[warn] why the feature should be explicitly enabled.
[warn]   implicit def rddToPairRDDFunctions[K: ClassTag, V: ClassTag](rdd: RDD[(K, V)]) =
[warn]                ^
```

scalac is suggesting that it's just best practice to explicitly enable certain language features by importing them where used.

This PR simply adds the imports it suggests (and squashes one other Java warning along the way). This leaves just deprecation warnings in the build.

Author: Sean Owen <sowen@cloudera.com>

Closes #404 from srowen/SPARK-1488 and squashes the following commits:

8598980 [Sean Owen] Quiet scalac warnings about language features by explicitly importing language features.
39bc831 [Sean Owen] Enable -feature in scalac to emit language feature warnings
changed title
SPARK-1374: PySpark API for SparkSQL

An initial API that exposes SparkSQL functionality in PySpark. A PythonRDD composed of dictionaries, with string keys and primitive values (boolean, float, int, long, string) can be converted into a SchemaRDD that supports sql queries.

```
from pyspark.context import SQLContext
sqlCtx = SQLContext(sc)
rdd = sc.parallelize([{"field1" : 1, "field2" : "row1"}, {"field1" : 2, "field2": "row2"}, {"field1" : 3, "field2": "row3"}])
srdd = sqlCtx.applySchema(rdd)
sqlCtx.registerRDDAsTable(srdd, "table1")
srdd2 = sqlCtx.sql("SELECT field1 AS f1, field2 as f2 from table1")
srdd2.collect()
```
The last line yields ```[{"f1" : 1, "f2" : "row1"}, {"f1" : 2, "f2": "row2"}, {"f1" : 3, "f2": "row3"}]```

Author: Ahir Reddy <ahirreddy@gmail.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #363 from ahirreddy/pysql and squashes the following commits:

0294497 [Ahir Reddy] Updated log4j properties to supress Hive Warns
307d6e0 [Ahir Reddy] Style fix
6f7b8f6 [Ahir Reddy] Temporary fix MIMA checker. Since we now assemble Spark jar with Hive, we don't want to check the interfaces of all of our hive dependencies
3ef074a [Ahir Reddy] Updated documentation because classes moved to sql.py
29245bf [Ahir Reddy] Cache underlying SchemaRDD instead of generating and caching PythonRDD
f2312c7 [Ahir Reddy] Moved everything into sql.py
a19afe4 [Ahir Reddy] Doc fixes
6d658ba [Ahir Reddy] Remove the metastore directory created by the HiveContext tests in SparkSQL
521ff6d [Ahir Reddy] Trying to get spark to build with hive
ab95eba [Ahir Reddy] Set SPARK_HIVE=true on jenkins
ded03e7 [Ahir Reddy] Added doc test for HiveContext
22de1d4 [Ahir Reddy] Fixed maven pyrolite dependency
e4da06c [Ahir Reddy] Display message if hive is not built into spark
227a0be [Michael Armbrust] Update API links. Fix Hive example.
58e2aa9 [Michael Armbrust] Build Docs for pyspark SQL Api.  Minor fixes.
4285340 [Michael Armbrust] Fix building of Hive API Docs.
38a92b0 [Michael Armbrust] Add note to future non-python developers about python docs.
337b201 [Ahir Reddy] Changed com.clearspring.analytics stream version from 2.4.0 to 2.5.1 to match SBT build, and added pyrolite to maven build
40491c9 [Ahir Reddy] PR Changes + Method Visibility
1836944 [Michael Armbrust] Fix comments.
e00980f [Michael Armbrust] First draft of python sql programming guide.
b0192d3 [Ahir Reddy] Added Long, Double and Boolean as usable types + unit test
f98a422 [Ahir Reddy] HiveContexts
79621cf [Ahir Reddy] cleaning up cruft
b406ba0 [Ahir Reddy] doctest formatting
20936a5 [Ahir Reddy] Added tests and documentation
e4d21b4 [Ahir Reddy] Added pyrolite dependency
79f739d [Ahir Reddy] added more tests
7515ba0 [Ahir Reddy] added more tests :)
d26ec5e [Ahir Reddy] added test
e9f5b8d [Ahir Reddy] adding tests
906d180 [Ahir Reddy] added todo explaining cost of creating Row object in python
251f99d [Ahir Reddy] for now only allow dictionaries as input
09b9980 [Ahir Reddy] made jrdd explicitly lazy
c608947 [Ahir Reddy] SchemaRDD now has all RDD operations
725c91e [Ahir Reddy] awesome row objects
55d1c76 [Ahir Reddy] return row objects
4fe1319 [Ahir Reddy] output dictionaries correctly
be079de [Ahir Reddy] returning dictionaries works
cd5f79f [Ahir Reddy] Switched to using Scala SQLContext
e948bd9 [Ahir Reddy] yippie
4886052 [Ahir Reddy] even better
c0fb1c6 [Ahir Reddy] more working
043ca85 [Ahir Reddy] working
5496f9f [Ahir Reddy] doesn't crash
b8b904b [Ahir Reddy] Added schema rdd class
67ba875 [Ahir Reddy] java to python, and python to java
bcc0f23 [Ahir Reddy] Java to python
ab6025d [Ahir Reddy] compiling
SPARK-1426: Make MLlib work with NumPy versions older than 1.7

Currently it requires NumPy 1.7 due to using the copyto method (http://docs.scipy.org/doc/numpy/reference/generated/numpy.copyto.html) for extracting data out of an array.
Replace it with a fallback

Author: Sandeep <sandeep@techaddict.me>

Closes #391 from techaddict/1426 and squashes the following commits:

d365962 [Sandeep] SPARK-1426: Make MLlib work with NumPy versions older than 1.7 Currently it requires NumPy 1.7 due to using the copyto method (http://docs.scipy.org/doc/numpy/reference/generated/numpy.copyto.html) for extracting data out of an array. Replace it with a fallback
SPARK-1501: Ensure assertions in Graph.apply are asserted.

The Graph.apply test in GraphSuite had some assertions in a closure in
a graph transformation. As a consequence, these assertions never
actually executed.  Furthermore, these closures had a reference to
(non-serializable) test harness classes because they called assert(),
which could be a problem if we proactively check closure serializability
in the future.

This commit simply changes the Graph.apply test to collect the graph
triplets so it can assert about each triplet from a map method.

Author: William Benton <willb@redhat.com>

Closes #415 from willb/graphsuite-nop-fix and squashes the following commits:

0b63658 [William Benton] Ensure assertions in Graph.apply are asserted.
[SPARK-1157][MLlib] L-BFGS Optimizer based on Breeze's implementation.

This PR uses Breeze's L-BFGS implement, and Breeze dependency has already been introduced by Xiangrui's sparse input format work in SPARK-1212. Nice work, @mengxr !

When use with regularized updater, we need compute the regVal and regGradient (the gradient of regularized part in the cost function), and in the currently updater design, we can compute those two values by the following way.

Let's review how updater works when returning newWeights given the input parameters.

w' = w - thisIterStepSize * (gradient + regGradient(w))  Note that regGradient is function of w!
If we set gradient = 0, thisIterStepSize = 1, then
regGradient(w) = w - w'

As a result, for regVal, it can be computed by

    val regVal = updater.compute(
      weights,
      new DoubleMatrix(initialWeights.length, 1), 0, 1, regParam)._2
and for regGradient, it can be obtained by

      val regGradient = weights.sub(
        updater.compute(weights, new DoubleMatrix(initialWeights.length, 1), 1, 1, regParam)._1)

The PR includes the tests which compare the result with SGD with/without regularization.

We did a comparison between LBFGS and SGD, and often we saw 10x less
steps in LBFGS while the cost of per step is the same (just computing
the gradient).

The following is the paper by Prof. Ng at Stanford comparing different
optimizers including LBFGS and SGD. They use them in the context of
deep learning, but worth as reference.
http://cs.stanford.edu/~jngiam/papers/LeNgiamCoatesLahiriProchnowNg2011.pdf

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #353 from dbtsai/dbtsai-LBFGS and squashes the following commits:

984b18e [DB Tsai] L-BFGS Optimizer based on Breeze's implementation. Also fixed indentation issue in GradientDescent optimizer.
Decision Tree documentation for MLlib programming guide

Added documentation for user to use the decision tree algorithms for classification and regression in Spark 1.0 release.

Apart from a general review, I need specific input on the following:
* I had to move a lot of the existing documentation under the *linear methods* umbrella to accommodate decision trees. I wonder if there is a better way to organize the programming guide given we are so close to the release.
* I have not looked closely at pyspark but I am wondering new mllib algorithms are automatically plugged in or do we need to some extra work to call mllib functions from pyspark. I will add to the pyspark examples based upon the advice I get.

cc: @mengxr, @hirakendu, @etrain, @atalwalkar

Author: Manish Amde <manish9ue@gmail.com>

Closes #402 from manishamde/tree_doc and squashes the following commits:

022485a [Manish Amde] more documentation
865826e [Manish Amde] minor: grammar
dbb0e5e [Manish Amde] minor improvements to text
b9ef6c4 [Manish Amde] basic decision tree code examples
6e297d7 [Manish Amde] added subsections
f427e84 [Manish Amde] renaming sections
9c0c4be [Manish Amde] split candidate
6925275 [Manish Amde] impurity and information gain
94fd2f9 [Manish Amde] more reorg
b93125c [Manish Amde] more subsection reorg
3ecb2ad [Manish Amde] minor text addition
1537dd3 [Manish Amde] added placeholders and some doc
d06511d [Manish Amde] basic skeleton
SPARK-1455: Better isolation for unit tests.

This is a simple first step towards avoiding running the Hive tests
whenever possible.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #420 from pwendell/test-isolation and squashes the following commits:

350c8af [Patrick Wendell] SPARK-1455: Better isolation for unit tests.
[FIX] update sbt-idea to version 1.6.0

I saw `No "scala-library*.jar" in Scala compiler library` error in IDEA. It seems upgrading `sbt-idea` to 1.6.0 fixed the problem.

Author: Xiangrui Meng <meng@databricks.com>

Closes #419 from mengxr/idea-plugin and squashes the following commits:

fb3c35f [Xiangrui Meng] update sbt-idea to version 1.6.0
[WIP] SPARK-1430: Support sparse data in Python MLlib

This PR adds a SparseVector class in PySpark and updates all the regression, classification and clustering algorithms and models to support sparse data, similar to MLlib. I chose to add this class because SciPy is quite difficult to install in many environments (more so than NumPy), but I plan to add support for SciPy sparse vectors later too, and make the methods work transparently on objects of either type.

On the Scala side, we keep Python sparse vectors sparse and pass them to MLlib. We always return dense vectors from our models.

Some to-do items left:
- [x] Support SciPy's scipy.sparse matrix objects when SciPy is available. We can easily add a function to convert these to our own SparseVector.
- [x] MLlib currently uses a vector with one extra column on the left to represent what we call LabeledPoint in Scala. Do we really want this? It may get annoying once you deal with sparse data since you must add/subtract 1 to each feature index when training. We can remove this API in 1.0 and use tuples for labeling.
- [x] Explain how to use these in the Python MLlib docs.

CC @mengxr, @joshrosen

Author: Matei Zaharia <matei@databricks.com>

Closes #341 from mateiz/py-ml-update and squashes the following commits:

d52e763 [Matei Zaharia] Remove no-longer-needed slice code and handle review comments
ea5a25a [Matei Zaharia] Fix remaining uses of copyto() after merge
b9f97a3 [Matei Zaharia] Fix test
1e1bd0f [Matei Zaharia] Add MLlib logistic regression example in Python
88bc01f [Matei Zaharia] Clean up inheritance of LinearModel in Python, and expose its parametrs
37ab747 [Matei Zaharia] Fix some examples and docs due to changes in MLlib API
da0f27e [Matei Zaharia] Added a MLlib K-means example and updated docs to discuss sparse data
c48e85a [Matei Zaharia] Added some tests for passing lists as input, and added mllib/tests.py to run-tests script.
a07ba10 [Matei Zaharia] Fix some typos and calculation of initial weights
74eefe7 [Matei Zaharia] Added LabeledPoint class in Python
889dde8 [Matei Zaharia] Support scipy.sparse matrices in all our algorithms and models
ab244d1 [Matei Zaharia] Allow SparseVectors to be initialized using a dict
a5d6426 [Matei Zaharia] Add linalg.py to run-tests script
0e7a3d8 [Matei Zaharia] Keep vectors sparse in Java when reading LabeledPoints
eaee759 [Matei Zaharia] Update regression, classification and clustering models for sparse data
2abbb44 [Matei Zaharia] Further work to get linear models working with sparse data
154f45d [Matei Zaharia] Update docs, name some magic values
881fef7 [Matei Zaharia] Added a sparse vector in Python and made Java-Python format more compact
[SQL] SPARK-1424 Generalize insertIntoTable functions on SchemaRDDs

This makes it possible to create tables and insert into them using the DSL and SQL for the scala and java apis.

Author: Michael Armbrust <michael@databricks.com>

Closes #354 from marmbrus/insertIntoTable and squashes the following commits:

6c6f227 [Michael Armbrust] Create random temporary files in python parquet unit tests.
f5e6d5c [Michael Armbrust] Merge remote-tracking branch 'origin/master' into insertIntoTable
765c506 [Michael Armbrust] Add to JavaAPI.
77b512c [Michael Armbrust] typos.
5c3ef95 [Michael Armbrust] use names for boolean args.
882afdf [Michael Armbrust] Change createTableAs to saveAsTable.  Clean up api annotations.
d07d94b [Michael Armbrust] Add tests, support for creating parquet files and hive tables.
fa3fe81 [Michael Armbrust] Make insertInto available on JavaSchemaRDD as well.  Add createTableAs function.
[SPARK-959] Updated SBT from 0.13.1 to 0.13.2

JIRA issue: [SPARK-959](https://spark-project.atlassian.net/browse/SPARK-959)

SBT 0.13.2 has been officially released. This version updated Ivy 2.0 to Ivy 2.3, which fixes [IVY-899](https://issues.apache.org/jira/browse/IVY-899). This PR also removed previous workaround.

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

Closes #426 from liancheng/updateSbt and squashes the following commits:

95e3dc8 [Cheng Lian] Updated SBT from 0.13.1 to 0.13.2 to fix SPARK-959
Make "spark logo" link refer to "/".

This is not an issue with the driver UI, but when you fire
up the history server, there's currently no way to go back to
the app listing page without editing the browser's location
field (since the logo's link points to the root of the
application's own UI - i.e. the "stages" tab).

The change just points the logo link to "/", which is the app
listing for the history server, and the stages tab for the
driver's UI.

Tested with both history server and live driver.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #408 from vanzin/web-ui-root and squashes the following commits:

1b60cb6 [Marcelo Vanzin] Make "spark logo" link refer to "/".
Loads test tables when running "sbt hive/console" without HIVE_DEV_HOME

When running Hive tests, the working directory is `$SPARK_HOME/sql/hive`, while when running `sbt hive/console`, it becomes `$SPARK_HOME`, and test tables are not loaded if `HIVE_DEV_HOME` is not defined.

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

Closes #417 from liancheng/loadTestTables and squashes the following commits:

7cea8d6 [Cheng Lian] Loads test tables when running "sbt hive/console" without HIVE_DEV_HOME
update spark.default.parallelism

actually, the value 8 is only valid in mesos fine-grained mode :
<code>
  override def defaultParallelism() = sc.conf.getInt("spark.default.parallelism", 8)
</code>

while in coarse-grained model including mesos coares-grained, the value of the property depending on core numbers!
<code>
override def defaultParallelism(): Int = {
   conf.getInt("spark.default.parallelism", math.max(totalCoreCount.get(), 2))
  }
</code>

Author: Chen Chao <crazyjvm@gmail.com>

Closes #389 from CrazyJvm/patch-2 and squashes the following commits:

84a7fe4 [Chen Chao] miss </li> at the end of every single line
04a9796 [Chen Chao] change format
ee0fae0 [Chen Chao] update spark.default.parallelism
SPARK-1310: Start adding k-fold cross validation to MLLib [adds kFold to MLUtils & fixes bug in BernoulliSampler]

Author: Holden Karau <holden@pigscanfly.ca>

Closes #18 from holdenk/addkfoldcrossvalidation and squashes the following commits:

208db9b [Holden Karau] Fix a bad space
e84f2fc [Holden Karau] Fix the test, we should be looking at the second element instead
6ddbf05 [Holden Karau] swap training and validation order
7157ae9 [Holden Karau] CR feedback
90896c7 [Holden Karau] New line
150889c [Holden Karau] Fix up error messages in the MLUtilsSuite
2cb90b3 [Holden Karau] Fix the names in kFold
c702a96 [Holden Karau] Fix imports in MLUtils
e187e35 [Holden Karau] Move { up to same line as whenExecuting(random) in RandomSamplerSuite.scala
c5b723f [Holden Karau] clean up
7ebe4d5 [Holden Karau] CR feedback, remove unecessary learners (came back during merge mistake) and insert an empty line
bb5fa56 [Holden Karau] extra line sadness
163c5b1 [Holden Karau] code review feedback 1.to -> 1 to and folds -> numFolds
5a33f1d [Holden Karau] Code review follow up.
e8741a7 [Holden Karau] CR feedback
b78804e [Holden Karau] Remove cross validation [TODO in another pull request]
91eae64 [Holden Karau] Consolidate things in mlutils
264502a [Holden Karau] Add a test for the bug that was found with BernoulliSampler not copying the complement param
dd0b737 [Holden Karau] Wrap long lines (oops)
c0b7fa4 [Holden Karau] Switch FoldedRDD to use BernoulliSampler and PartitionwiseSampledRDD
08f8e4d [Holden Karau] Fix BernoulliSampler to respect complement
a751ec6 [Holden Karau] Add k-fold cross validation to MLLib
SPARK-1497. Fix scalastyle warnings in YARN, Hive code

(I wasn't sure how to automatically set `SPARK_YARN=true` and `SPARK_HIVE=true` when running scalastyle, but these are the errors that turn up.)

Author: Sean Owen <sowen@cloudera.com>

Closes #413 from srowen/SPARK-1497 and squashes the following commits:

f0c9318 [Sean Owen] Fix more scalastyle warnings in yarn
80bf4c3 [Sean Owen] Add YARN alpha / YARN profile to scalastyle check
026319c [Sean Owen] Fix scalastyle warnings in YARN, Hive code
Minor addition to SPARK-1497