This is a follow-up patch to #6441.

Author: Andrew Or <andrew@databricks.com>

Closes #6510 from andrewor14/extends-funsuite-check and squashes the following commits:

6618b46 [Andrew Or] Exempt SparkSinkSuite from the FunSuite check
99d02ac [Andrew Or] Merge branch 'master' of github.com:apache/spark into extends-funsuite-check
48874dd [Andrew Or] Guard against direct uses of FunSuite / FunSuiteLike

cc JoshRosen
Thanks for noticing this!

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #6509 from brkyvz/sample-perf-reg and squashes the following commits:

497465d [Burak Yavuz] addressed code review
293f95f [Burak Yavuz] [SPARK-7957] Preserve partitioning when using randomSplit

The first line had only two dashes (--) instead of three(---). Because of this missing dash(-), 'jekyll build' command was not converting configuration.md to _site/configuration.html

Author: Taka Shinagawa <taka.epsilon@gmail.com>

Closes #6513 from mrt/docfix3 and squashes the following commits:

c470e2c [Taka Shinagawa] Added a missing dash(-) preventing jekyll from converting configuration.md to html format

This patch fixes a build break in maven caused by #6441.

Note that this patch reverts the changes in flume-sink because
this module does not currently depend on Spark core, but the
tests require it. There is not an easy way to make this work
because mvn test dependencies are not transitive (MNG-1378).

For now, we will leave the one test suite in flume-sink out
until we figure out a better solution. This patch is mainly
intended to unbreak the maven build.

Author: Andrew Or <andrew@databricks.com>

Closes #6511 from andrewor14/fix-build-mvn and squashes the following commits:

3d53643 [Andrew Or] [HOT FIX #6441] Fix maven build failures

Tests compile in SBT but not Maven.

Author: Ram Sriharsha <rsriharsha@hw11853.local>

Closes #6443 from harsha2010/SPARK-6013 and squashes the following commits:

732506e [Ram Sriharsha] Code Review Feedback
121c211 [Ram Sriharsha] python style fix
5f9b8c3 [Ram Sriharsha] python style fixes
925ca86 [Ram Sriharsha] Simple Params Example
8b372b1 [Ram Sriharsha] GBT Example
965ec14 [Ram Sriharsha] Random Forest Example

cc davies

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #6507 from shivaram/sparkr-init and squashes the following commits:

6fdd169 [Shivaram Venkataraman] Create SparkContext in sparkRSQL init

Author: Holden Karau <holden@pigscanfly.ca>

Closes #6464 from holdenk/SPARK-7910-expose-partitioner-information-in-javardd and squashes the following commits:

de1e644 [Holden Karau] Fix the test to get the partitioner
bdb31cc [Holden Karau] Add Mima exclude for the new method
347ef4c [Holden Karau] Add a quick little test for the partitioner JavaAPI
f49dca9 [Holden Karau] Add partitoner information to JavaRDDLike and fix some whitespace

This PR makes the types module in `pyspark/sql/types` work with pylint static analysis by removing the dynamic naming of the `pyspark/sql/_types` module to `pyspark/sql/types`.

Tests are now loaded using `$PYSPARK_DRIVER_PYTHON -m module` rather than `$PYSPARK_DRIVER_PYTHON module.py`. The old method adds the location of `module.py` to `sys.path`, so this change prevents accidental use of relative paths in Python.

Author: Michael Nazario <mnazario@palantir.com>

Closes #6439 from mnazario/feature/SPARK-7899 and squashes the following commits:

366ef30 [Michael Nazario] Remove hack on random.py
bb8b04d [Michael Nazario] Make doctests consistent with other tests
6ee4f75 [Michael Nazario] Change test scripts to use "-m"
673528f [Michael Nazario] Move _types back to types

This PR adds a new SparkR programming guide at the top-level. This will be useful for R users as our APIs don't directly match the Scala/Python APIs and as we need to explain SparkR without using RDDs as examples etc.

cc rxin davies pwendell

cc cafreeman -- Would be great if you could also take a look at this !

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #6490 from shivaram/sparkr-guide and squashes the following commits:

d5ff360 [Shivaram Venkataraman] Add a section on HiveContext, HQL queries
408dce5 [Shivaram Venkataraman] Fix link
dbb86e3 [Shivaram Venkataraman] Fix minor typo
9aff5e0 [Shivaram Venkataraman] Address comments, use dplyr-like syntax in example
d09703c [Shivaram Venkataraman] Fix default argument in read.df
ea816a1 [Shivaram Venkataraman] Add a new SparkR programming guide Also update write.df, read.df to handle defaults better

Right now `unit-tests.log` are not of much value because we can't tell where the test boundaries are easily. This patch adds log statements before and after each test to outline the test boundaries, e.g.:

```
===== TEST OUTPUT FOR o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' =====

15/05/27 12:36:39.596 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO SparkContext: Starting job: count at KryoSerializerSuite.scala:230
15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Got job 3 (count at KryoSerializerSuite.scala:230) with 4 output partitions (allowLocal=false)
15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Final stage: ResultStage 3(count at KryoSerializerSuite.scala:230)
15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Parents of final stage: List()
15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Missing parents: List()
15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Submitting ResultStage 3 (ParallelCollectionRDD[5] at parallelize at KryoSerializerSuite.scala:230), which has no missing parents

...

15/05/27 12:36:39.624 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO DAGScheduler: Job 3 finished: count at KryoSerializerSuite.scala:230, took 0.028563 s
15/05/27 12:36:39.625 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO KryoSerializerSuite:

***** FINISHED o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' *****

...
```

Author: Andrew Or <andrew@databricks.com>

Closes #6441 from andrewor14/demarcate-tests and squashes the following commits:

879b060 [Andrew Or] Fix compile after rebase
d622af7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests
017c8ba [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests
7790b6c [Andrew Or] Fix tests after logical merge conflict
c7460c0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests
c43ffc4 [Andrew Or] Fix tests?
8882581 [Andrew Or] Fix tests
ee22cda [Andrew Or] Fix log message
fa9450e [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests
12d1e1b [Andrew Or] Various whitespace changes (minor)
69cbb24 [Andrew Or] Make all test suites extend SparkFunSuite instead of FunSuite
bbce12e [Andrew Or] Fix manual things that cannot be covered through automation
da0b12f [Andrew Or] Add core tests as dependencies in all modules
f7d29ce [Andrew Or] Introduce base abstract class for all test suites

[SPARK-7940] Enforce whitespace checking for DO, TRY, CATCH, FINALLY, MATCH, LARROW, RARROW in style checker.

…

Author: Reynold Xin <rxin@databricks.com>

Closes #6491 from rxin/more-whitespace and squashes the following commits:

f6e63dc [Reynold Xin] [SPARK-7940] Enforce whitespace checking for DO, TRY, CATCH, FINALLY, MATCH, LARROW, RARROW in style checker.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #6497 from MechCoder/spark-7946 and squashes the following commits:

2fdd0a3 [MechCoder] Add non-regression test
8c988c6 [MechCoder] [SPARK-7946] DecayFactor wrongly set in StreamingKMeans

[SQL] [TEST] [MINOR] Uses a temporary log4j.properties in HiveThriftServer2Test to ensure expected logging behavior

The `HiveThriftServer2Test` relies on proper logging behavior to assert whether the Thrift server daemon process is started successfully. However, some other jar files listed in the classpath may potentially contain an unexpected Log4J configuration file which overrides the logging behavior.

This PR writes a temporary `log4j.properties` and prepend it to driver classpath before starting the testing Thrift server process to ensure proper logging behavior.

cc andrewor14 yhuai

Author: Cheng Lian <lian@databricks.com>

Closes #6493 from liancheng/override-log4j and squashes the following commits:

c489e0e [Cheng Lian] Fixes minor Scala styling issue
b46ef0d [Cheng Lian] Uses a temporary log4j.properties in HiveThriftServer2Test to ensure expected logging behavior

When starting `HiveThriftServer2` via `startWithContext`, property `spark.sql.hive.version` isn't set. This causes Simba ODBC driver 1.0.8.1006 behaves differently and fails simple queries.

Hive2 JDBC driver works fine in this case. Also, when starting the server with `start-thriftserver.sh`, both Hive2 JDBC driver and Simba ODBC driver works fine.

Please refer to [SPARK-7950] [1] for details.

[1]: https://issues.apache.org/jira/browse/SPARK-7950

Author: Cheng Lian <lian@databricks.com>

Closes #6500 from liancheng/odbc-bugfix and squashes the following commits:

051e3a3 [Cheng Lian] Fixes import order
3a97376 [Cheng Lian] Sets spark.sql.hive.version in HiveThriftServer2.startWithContext()

[SPARK-7524] [SPARK-7846] add configs for keytab and principal, pass these two configs with different way in different modes

* As spark now supports long running service by updating tokens for namenode, but only accept parameters passed with "--k=v" format which is not very convinient. This patch add spark.* configs in properties file and system property.

*  --principal and --keytabl options are passed to client but when we started thrift server or spark-shell these two are also passed into the Main class (org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 and org.apache.spark.repl.Main).
In these two main class, arguments passed in will be processed with some 3rd libraries, which will lead to some error: "Invalid option: --principal" or "Unrecgnised option: --principal".
We should pass these command args in different forms, say system properties.

Author: WangTaoTheTonic <wangtao111@huawei.com>

Closes #6051 from WangTaoTheTonic/SPARK-7524 and squashes the following commits:

e65699a [WangTaoTheTonic] change logic to loadEnvironments
ebd9ea0 [WangTaoTheTonic] merge master
ecfe43a [WangTaoTheTonic] pass keytab and principal seperately in different mode
33a7f40 [WangTaoTheTonic] expand the use of the current configs
08bb4e8 [WangTaoTheTonic] fix wrong cite
73afa64 [WangTaoTheTonic] add configs for keytab and principal, move originals to internal

[SPARK-7863] [CORE] Create SimpleDateFormat for every SimpleDateParam instance because it's not thread-safe

SimpleDateFormat is not thread-safe. This PR creates new `SimpleDateFormat` for each `SimpleDateParam` instance.

Author: zsxwing <zsxwing@gmail.com>

Closes #6406 from zsxwing/SPARK-7863 and squashes the following commits:

aeed4c1 [zsxwing] Rewrite SimpleDateParam
8cdd986 [zsxwing] Inline formats
9680a15 [zsxwing] Create SimpleDateFormat for each SimpleDateParam instance because it's not thread-safe

Add alias names for supported cipher suites to the sample SSL configuration.

The IBM JSSE provider reports its cipher suite with an SSL_ prefix, but accepts TLS_ prefixed suite names as an alias.  However, Jetty filters the requested ciphers based on the provider's reported supported suites, so the TLS_ versions are never passed through to JSSE causing an SSL handshake failure.

Author: Tim Ellison <t.p.ellison@gmail.com>

Closes #6282 from tellison/SSLFailure and squashes the following commits:

8de8a3e [Tim Ellison] Update SecurityManagerSuite with new expected suite names
96158b2 [Tim Ellison] Update the sample configs to use ciphers that are common to both the Oracle and IBM security providers.
705421b [Tim Ellison] Merge branch 'master' of github.com:tellison/spark into SSLFailure
68b9425 [Tim Ellison] Merge branch 'master' of https://github.com/apache/spark into SSLFailure
b0c35f6 [Tim Ellison] [CORE] Add aliases used for cipher suites in IBM provider

[SPARK-7912] [SPARK-7921] [MLLIB] Update OneHotEncoder to handle ML attributes and change includeFirst to dropLast

This PR contains two major changes to `OneHotEncoder`:

1. more robust handling of ML attributes. If the input attribute is unknown, we look at the values to get the max category index
2. change `includeFirst` to `dropLast` and leave the default to `true`. There are couple benefits:

    a. consistent with other tutorials of one-hot encoding (or dummy coding) (e.g., http://www.ats.ucla.edu/stat/mult_pkg/faq/general/dummy.htm)
    b. keep the indices unmodified in the output vector. If we drop the first, all indices will be shifted by 1.
    c. If users use `StringIndex`, the last element is the least frequent one.

Sorry for including two changes in one PR! I'll update the user guide in another PR.

jkbradley sryza

Author: Xiangrui Meng <meng@databricks.com>

Closes #6466 from mengxr/SPARK-7912 and squashes the following commits:

a280dca [Xiangrui Meng] fix tests
d8f234d [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7912
171b276 [Xiangrui Meng] mention the difference between our impl vs sklearn's
00dfd96 [Xiangrui Meng] update OneHotEncoder in Python
208ddad [Xiangrui Meng] update OneHotEncoder to handle ML attributes and change includeFirst to dropLast

This is the last batch of changes to complete SPARK-7929.

Previous related PRs:
https://github.com/apache/spark/pull/6480
https://github.com/apache/spark/pull/6478
https://github.com/apache/spark/pull/6477
https://github.com/apache/spark/pull/6476
https://github.com/apache/spark/pull/6475
https://github.com/apache/spark/pull/6474
https://github.com/apache/spark/pull/6473

Author: Reynold Xin <rxin@databricks.com>

Closes #6487 from rxin/whitespace-lint and squashes the following commits:

b33d43d [Reynold Xin] [SPARK-7929] Turn whitespace checker on for more token types.

Attempts to restart the socket receiver when it is supposed to be stopped causes undesirable error messages.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #6483 from tdas/SPARK-7931 and squashes the following commits:

09aeee1 [Tathagata Das] Do not restart receiver when stopped

Expose user/item factors in DataFrames. This is to be more consistent with the pipeline API. It also helps maintain consistent APIs across languages. This PR also removed fitting params from `ALSModel`.

coderxiang

Author: Xiangrui Meng <meng@databricks.com>

Closes #6468 from mengxr/SPARK-7922 and squashes the following commits:

7bfb1d5 [Xiangrui Meng] update ALSModel in PySpark
1ba5607 [Xiangrui Meng] use DataFrames for user/item factors in ALS

Shutdown hook for temp directories had priority 100 while SparkContext was 50. So the local root directory was deleted before SparkContext was shutdown. This leads to scary errors on running jobs, at the time of shutdown. This is especially a problem when running streaming examples, where Ctrl-C is the only way to shutdown.

The fix in this PR is to make the temp directory shutdown priority lower than SparkContext, so that the temp dirs are the last thing to get deleted, after the SparkContext has been shut down. Also, the DiskBlockManager shutdown priority is change from default 100 to temp_dir_prio + 1, so that it gets invoked just before all temp dirs are cleared.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #6482 from tdas/SPARK-7930 and squashes the following commits:

d7cbeb5 [Tathagata Das] Removed unnecessary line
1514d0b [Tathagata Das] Fixed shutdown hook priorities

The existing code rounds down to the nearest percent when computing the proportion
of a task's time that was spent on each phase of execution, and then computes
the scheduler delay proportion as 100 - sum(all other proportions).  As a result,
a few extra percent can end up in the scheduler delay. This commit eliminates
the rounding so that the time visualizations correspond properly to the real times.

sarutak If you could take a look at this, that would be great! Not sure if there's a good
reason to round here that I missed.

cc shivaram

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #6484 from kayousterhout/SPARK-7932 and squashes the following commits:

1723cc4 [Kay Ousterhout] [SPARK-7932] Fix misleading scheduler delay visualization

`make clean html` under `python/doc` returns
~~~
/Users/meng/src/spark/python/pyspark/ml/evaluation.py:docstring of pyspark.ml.evaluation.RegressionEvaluator.setParams:3: WARNING: Definition list ends without a blank line; unexpected unindent.
~~~

harsha2010

Author: Xiangrui Meng <meng@databricks.com>

Closes #6469 from mengxr/fix-regression-evaluator-doc and squashes the following commits:

91e2dad [Xiangrui Meng] fix RegressionEvaluator doc

Switch to the official Pyrolite release from the one published under `org.spark-project`. Thanks irmen for making the releases on Maven Central. We didn't upgrade to 4.6 because we don't have enough time for QA. I excludes `serpent` from its dependencies because we don't use it in Spark.
~~~
[info]   +-net.jpountz.lz4:lz4:1.3.0
[info]   +-net.razorvine:pyrolite:4.4
[info]   +-net.sf.py4j:py4j:0.8.2.1
~~~

davies

Author: Xiangrui Meng <meng@databricks.com>

Closes #6472 from mengxr/SPARK-7926 and squashes the following commits:

7b3c6bf [Xiangrui Meng] use the official Pyrolite release

So we can enable a whitespace enforcement rule in the style checker to save code review time.

Author: Reynold Xin <rxin@databricks.com>

Closes #6474 from rxin/whitespace-graphx and squashes the following commits:

4d3cd26 [Reynold Xin] Fixed tests.
869dde4 [Reynold Xin] [SPARK-7927] whitespace fixes for GraphX.

So we can enable a whitespace enforcement rule in the style checker to save code review time.

Author: Reynold Xin <rxin@databricks.com>

Closes #6473 from rxin/whitespace-core and squashes the following commits:

058195d [Reynold Xin] Fixed tests.
fce11e9 [Reynold Xin] [SPARK-7927] whitespace fixes for core.

So we can enable a whitespace enforcement rule in the style checker to save code review time.

Author: Reynold Xin <rxin@databricks.com>

Closes #6476 from rxin/whitespace-catalyst and squashes the following commits:

650409d [Reynold Xin] Fixed tests.
51a9e5d [Reynold Xin] [SPARK-7927] whitespace fixes for Catalyst module.

Author: Reynold Xin <rxin@databricks.com>

Closes #6480 from rxin/whitespace-example and squashes the following commits:

8a4a3d4 [Reynold Xin] [SPARK-7929] Remove Bagel examples & whitespace fix for examples.

So we can enable a whitespace enforcement rule in the style checker to save code review time.

Author: Reynold Xin <rxin@databricks.com>

Closes #6477 from rxin/whitespace-sql-core and squashes the following commits:

ce6e369 [Reynold Xin] Fixed tests.
6095fed [Reynold Xin] [SPARK-7927] whitespace fixes for SQL core.

rxin

Author: Xiangrui Meng <meng@databricks.com>

Closes #6481 from mengxr/mllib-scalastyle and squashes the following commits:

3ca4d61 [Xiangrui Meng] revert scalastyle config
30961ba [Xiangrui Meng] adjust spaces in mllib/test
571b5c5 [Xiangrui Meng] fix spaces in mllib

There are too many extra call method `getCacheLocs` for `DAGScheduler`, which includes Akka communication.
To improve `DAGScheduler` performance, suppress extra calling the method.

In my application with over 1200 stages, the execution time became 3.8 min from 8.5 min with my patch.

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

Closes #6352 from ueshin/issues/SPARK-7826 and squashes the following commits:

3d4d036 [Takuya UESHIN] Modify a test and the documentation.
10b1b22 [Takuya UESHIN] Simplify the unit test.
d858b59 [Takuya UESHIN] Move the storageLevel check inside the if (!cacheLocs.contains(rdd.id)) block.
6f3125c [Takuya UESHIN] Fix scalastyle.
b9c835c [Takuya UESHIN] Put the condition that checks if the RDD has uncached partition or not into variable for readability.
f87f2ec [Takuya UESHIN] Get cached locations from block manager only if the storage level of the RDD is not StorageLevel.NONE.
8248386 [Takuya UESHIN] Revert "Suppress extra calling getCacheLocs."
a4d944a [Takuya UESHIN] Add an unit test.
9a80fad [Takuya UESHIN] Suppress extra calling getCacheLocs.

Looks like this was added by accident when pwendell merged a commit back in September: fe2b1d6a

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #6485 from kayousterhout/SPARK-7933 and squashes the following commits:

7c6164a [Kay Ousterhout] [SPARK-7933] Remove Patrick's username/pw from merge script

So we can enable a whitespace enforcement rule in the style checker to save code review time.

Author: Reynold Xin <rxin@databricks.com>

Closes #6478 from rxin/whitespace-hive and squashes the following commits:

e01b0e0 [Reynold Xin] Fixed tests.
a3bba22 [Reynold Xin] [SPARK-7927] whitespace fixes for Hive and ThriftServer.

So we can enable a whitespace enforcement rule in the style checker to save code review time.

Author: Reynold Xin <rxin@databricks.com>

Closes #6475 from rxin/whitespace-streaming and squashes the following commits:

810dae4 [Reynold Xin] Fixed tests.
89068ad [Reynold Xin] [SPARK-7927] whitespace fixes for streaming.

CC jkbradley

Author: Xusen Yin <yinxusen@gmail.com>

Closes #6451 from yinxusen/SPARK-7577 and squashes the following commits:

e2dc32e [Xusen Yin] rename colums
e350e49 [Xusen Yin] add all demos
006ddf1 [Xusen Yin] add java test
3238481 [Xusen Yin] add bucketizer

https://issues.apache.org/jira/browse/SPARK-7853

This fixes the problem introduced by my change in https://github.com/apache/spark/pull/6435, which causes that Hive Context fails to create in spark shell because of the class loader issue.

Author: Yin Huai <yhuai@databricks.com>

Closes #6459 from yhuai/SPARK-7853 and squashes the following commits:

37ad33e [Yin Huai] Do not use hiveQlTable at all.
47cdb6d [Yin Huai] Move hiveconf.set to the end of setConf.
005649b [Yin Huai] Update comment.
35d86f3 [Yin Huai] Access TTable directly to make sure Hive will not internally use any metastore utility functions.
3737766 [Yin Huai] Recursively find all jars.