Added a new test suite to make sure Java DF programs can use varargs properly.
Also moved all suites into test.org.apache.spark package to make sure the suites also test for method visibility.

Author: Reynold Xin <rxin@databricks.com>

Closes #4751 from rxin/df-tests and squashes the following commits:

1e8b8e4 [Reynold Xin] Fixed imports and renamed JavaAPISuite.
a6ca53b [Reynold Xin] [SPARK-5904][SQL] DataFrame Java API test suites.

**NOTICE** Do NOT merge this, as we're waiting for #3881 to be merged.

`HiveThriftServer2Suite` has been notorious for its flakiness for a while. This was mostly due to spawning and communicate with external server processes. This PR revamps this test suite for better robustness:

1. Fixes a racing condition occurred while using `tail -f` to check log file

   It's possible that the line we are looking for has already been printed into the log file before we start the `tail -f` process. This PR uses `tail -n +0 -f` to ensure all lines are checked.

2. Retries up to 3 times if the server fails to start

   In most of the cases, the server fails to start because of port conflict. This PR no longer asks the system to choose an available TCP port, but uses a random port first, and retries up to 3 times if the server fails to start.

3. A server instance is reused among all test cases within a single suite

   The original `HiveThriftServer2Suite` is splitted into two test suites, `HiveThriftBinaryServerSuite` and `HiveThriftHttpServerSuite`. Each suite starts a `HiveThriftServer2` instance and reuses it for all of its test cases.

**TODO**

- [ ] Starts the Thrift server in foreground once #3881 is merged (adding `--foreground` flag to `spark-daemon.sh`)

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Author: Cheng Lian <lian@databricks.com>

Closes #4720 from liancheng/revamp-thrift-server-tests and squashes the following commits:

d6c80eb [Cheng Lian] Relaxes server startup timeout
6f14eb1 [Cheng Lian] Revamped HiveThriftServer2Suite for robustness

One can early stop if the decrease in error rate is lesser than a certain tol or if the error increases if the training data is overfit.

This introduces a new method runWithValidation which takes in a pair of RDD's , one for the training data and the other for the validation.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #4677 from MechCoder/spark-5436 and squashes the following commits:

1bb21d4 [MechCoder] Combine regression and classification tests into a single one
e4d799b [MechCoder] Addresses indentation and doc comments
b48a70f [MechCoder] COSMIT
b928a19 [MechCoder] Move validation while training section under usage tips
fad9b6e [MechCoder] Made the following changes 1. Add section to documentation 2. Return corresponding to bestValidationError 3. Allow negative tolerance.
55e5c3b [MechCoder] One liner for prevValidateError
3e74372 [MechCoder] TST: Add test for classification
77549a9 [MechCoder] [SPARK-5436] Validate GradientBoostedTrees using runWithValidation

Author: Davies Liu <davies@databricks.com>

Closes #4745 from davies/fix_zip and squashes the following commits:

2124b2c [Davies Liu] Update tests.py
b5c828f [Davies Liu] increase the number of records
c1e40fd [Davies Liu] fix zip with two RDDs with AutoBatchedSerializer

Author: Michael Armbrust <michael@databricks.com>

Closes #4746 from marmbrus/hiveLock and squashes the following commits:

8b871cf [Michael Armbrust] [SPARK-5952][SQL] Lock when using hive metastore client

Add Slf4jSink to Spark Metrics using Coda Hale's SlfjReporter.
This sends metrics to log4j, allowing spark users to reuse log4j pipeline for metrics collection.

Reviewed existing unit tests and didn't see any sink-related tests. Please advise on if tests should be added.

Author: Judy <judynash@microsoft.com>
Author: judynash <judynash@microsoft.com>

Closes #4644 from judynash/master and squashes the following commits:

57ef214 [judynash] doc clarification and indent fixes
a751a66 [Judy] Spark-5708: Add Slf4jSink to Spark Metrics

Variance is calculated on labels/responses.

Author: Xiangrui Meng <meng@databricks.com>

Closes #4740 from mengxr/patch-1 and squashes the following commits:

673317b [Xiangrui Meng] [MLLIB] Change x_i to y_i in Variance's user guide

For screenshot see: https://issues.apache.org/jira/browse/SPARK-5965
This was caused by 20a60131.

Author: Andrew Or <andrew@databricks.com>

Closes #4739 from andrewor14/user-jar-blocker and squashes the following commits:

23c4a9e [Andrew Or] Use right argument

Patch should be self-explanatory
pwendell JoshRosen

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

Closes #4741 from tdas/SPARK-5967 and squashes the following commits:

653b5bb [Tathagata Das] Fixed the fix and added test
e2de972 [Tathagata Das] Clear stages which have no corresponding active jobs.

Author: Michael Armbrust <michael@databricks.com>

Closes #4738 from marmbrus/udtRepart and squashes the following commits:

c06d7b5 [Michael Armbrust] fix compilation
91c8829 [Michael Armbrust] [SQL][SPARK-5532] Repartition should not use external rdd representation

Author: Michael Armbrust <michael@databricks.com>

Closes #4736 from marmbrus/asExprs and squashes the following commits:

5ba97e4 [Michael Armbrust] [SPARK-5910][SQL] Support for as in selectExpr

Please refer to the [JIRA ticket] [1] for the motivation.

[1]: https://issues.apache.org/jira/browse/SPARK-5968

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Author: Cheng Lian <lian@databricks.com>

Closes #4744 from liancheng/spark-5968 and squashes the following commits:

caac6a8 [Cheng Lian] Suppresses ParquetOutputCommitter WARN logs

* Removed SVD code from examples.
* Corrected Java API doc link.
* Updated variable names: `AtransposeA` -> `ata`.
* Minor changes.

brkyvz

Author: Xiangrui Meng <meng@databricks.com>

Closes #4737 from mengxr/update-block-matrix-user-guide and squashes the following commits:

70f53ac [Xiangrui Meng] update block matrix user guide

Author: Michael Armbrust <michael@databricks.com>

Closes #4684 from marmbrus/explainAnalysis and squashes the following commits:

afbaa19 [Michael Armbrust] fix python
d93278c [Michael Armbrust] fix hive
e5fa0a4 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into explainAnalysis
52119f2 [Michael Armbrust] more tests
82a5431 [Michael Armbrust] fix tests
25753d2 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into explainAnalysis
aee1e6a [Michael Armbrust] fix hive
b23a844 [Michael Armbrust] newline
de8dc51 [Michael Armbrust] more comments
acf620a [Michael Armbrust] [SPARK-5873][SQL] Show partially analyzed plans in query execution

JIRA: https://issues.apache.org/jira/browse/SPARK-5935

Author: Yin Huai <yhuai@databricks.com>
Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #4710 from yhuai/jsonMapType and squashes the following commits:

3e40390 [Yin Huai] Remove unnecessary changes.
f8e6267 [Yin Huai] Fix test.
baa36e3 [Yin Huai] Accept MapType in the schema provided to jsonFile/jsonRDD.

Fixes:
* typo in Scala example
* Removed comment "usually applied on sparse data" since that is debatable
* small edits to text for clarity

CC: avulanov  I noticed a typo post-hoc and ended up making a few small edits.  Do the changes look OK?

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4732 from jkbradley/chisqselector-docs and squashes the following commits:

9656a3b [Joseph K. Bradley] added Java example for ChiSqSelector to guide
3f3f9f4 [Joseph K. Bradley] small fixes to ChiSqSelector docs

Added description of ChiSqSelector and few words about feature selection in general. I could add a code example, however it would not look reasonable in the absence of feature discretizer or a dataset in the `data` folder that has redundant features.

Author: Alexander Ulanov <nashb@yandex.ru>

Closes #4709 from avulanov/SPARK-5912 and squashes the following commits:

19a8a4e [Alexander Ulanov] Addressing reviewers comments @jkbradley
58d9e4d [Alexander Ulanov] Addressing reviewers comments @jkbradley
eb6b9fe [Alexander Ulanov] Typo
2921a1d [Alexander Ulanov] ChiSqSelector example of use
c845350 [Alexander Ulanov] ChiSqSelector docs

Add parameter parsing in FPGrowth example app in Scala and Java
And a sample data file is added in data/mllib folder

Author: Jacky Li <jacky.likun@huawei.com>

Closes #4714 from jackylk/parameter and squashes the following commits:

8c478b3 [Jacky Li] fix according to comments
3bb74f6 [Jacky Li] make FPGrowth exampl app take parameters
f0e4d10 [Jacky Li] make FPGrowth exampl app take parameters

https://issues.apache.org/jira/browse/SPARK-5724

In AkkaUtil, we set several failure detector related the parameters as following

```
al akkaConf = ConfigFactory.parseMap(conf.getAkkaConf.toMap[String, String])
      .withFallback(akkaSslConfig).withFallback(ConfigFactory.parseString(
      s"""
      |akka.daemonic = on
      |akka.loggers = [""akka.event.slf4j.Slf4jLogger""]
      |akka.stdout-loglevel = "ERROR"
      |akka.jvm-exit-on-fatal-error = off
      |akka.remote.require-cookie = "$requireCookie"
      |akka.remote.secure-cookie = "$secureCookie"
      |akka.remote.transport-failure-detector.heartbeat-interval = $akkaHeartBeatInterval s
      |akka.remote.transport-failure-detector.acceptable-heartbeat-pause = $akkaHeartBeatPauses s
      |akka.remote.transport-failure-detector.threshold = $akkaFailureDetector
      |akka.actor.provider = "akka.remote.RemoteActorRefProvider"
      |akka.remote.netty.tcp.transport-class = "akka.remote.transport.netty.NettyTransport"
      |akka.remote.netty.tcp.hostname = "$host"
      |akka.remote.netty.tcp.port = $port
      |akka.remote.netty.tcp.tcp-nodelay = on
      |akka.remote.netty.tcp.connection-timeout = $akkaTimeout s
      |akka.remote.netty.tcp.maximum-frame-size = ${akkaFrameSize}B
      |akka.remote.netty.tcp.execution-pool-size = $akkaThreads
      |akka.actor.default-dispatcher.throughput = $akkaBatchSize
      |akka.log-config-on-start = $logAkkaConfig
      |akka.remote.log-remote-lifecycle-events = $lifecycleEvents
      |akka.log-dead-letters = $lifecycleEvents
      |akka.log-dead-letters-during-shutdown = $lifecycleEvents
      """.stripMargin))

```

Actually, we do not have any parameter naming "akka.remote.transport-failure-detector.threshold"
see: http://doc.akka.io/docs/akka/2.3.4/general/configuration.html
what we have is "akka.remote.watch-failure-detector.threshold"

Author: CodingCat <zhunansjtu@gmail.com>

Closes #4512 from CodingCat/SPARK-5724 and squashes the following commits:

bafe56e [CodingCat] fix the grammar in configuration doc
338296e [CodingCat] remove failure-detector related info
8bfcfd4 [CodingCat] fix the misconfiguration in AkkaUtils

Author: Saisai Shao <saisai.shao@intel.com>

Closes #4722 from jerryshao/SPARK-5943 and squashes the following commits:

1b01233 [Saisai Shao] Update the test to use new API to reduce the warning

Author: Makoto Fukuhara <fukuo33@gmail.com>

Closes #4724 from fukuo33/fix-typo and squashes the following commits:

8c806b9 [Makoto Fukuhara] fix typo.

Instead of storing a strong reference to accumulators, I've replaced this with a weak reference and updated any code that uses these accumulators to check whether the reference resolves before using the accumulator. A weak reference will be cleared when there is no longer an existing copy of the variable versus using a soft reference in which case accumulators would only be cleared when the GC explicitly ran out of memory.

Author: Ilya Ganelin <ilya.ganelin@capitalone.com>

Closes #4021 from ilganeli/SPARK-3885 and squashes the following commits:

4ba9575 [Ilya Ganelin]  Fixed error in test suite
8510943 [Ilya Ganelin] Extra code
bb76ef0 [Ilya Ganelin] File deleted somehow
283a333 [Ilya Ganelin] Added cleanup method for accumulators to remove stale references within Accumulators.original to accumulators that are now out of scope
345fd4f [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885
7485a82 [Ilya Ganelin] Fixed build error
c8e0f2b [Ilya Ganelin] Added working test for accumulator garbage collection
94ce754 [Ilya Ganelin] Still not being properly garbage collected
8722b63 [Ilya Ganelin] Fixing gc test
7414a9c [Ilya Ganelin] Added test for accumulator garbage collection
18d62ec [Ilya Ganelin] Updated to throw Exception when accessing a GCd accumulator
9a81928 [Ilya Ganelin] Reverting permissions changes
28f705c [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885
b820ab4b [Ilya Ganelin] reset
d78f4bf [Ilya Ganelin] Removed obsolete comment
0746e61 [Ilya Ganelin] Updated DAGSchedulerSUite to fix bug
3350852 [Ilya Ganelin] Updated DAGScheduler and Suite to correctly use new implementation of WeakRef Accumulator storage
c49066a [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885
cbb9023 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-3885
a77d11b [Ilya Ganelin] Updated Accumulators class to store weak references instead of strong references to allow garbage collection of old accumulators

...th RangePartitioner

Author: Aaron Josephs <ajoseph4@binghamton.edu>

Closes #1381 from aaronjosephs/PLAT-911 and squashes the following commits:

e30ade5 [Aaron Josephs] [SPARK-911] allow efficient queries for a range if RDD is partitioned with RangePartitioner

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

Closes #4717 from chenghao-intel/typo1 and squashes the following commits:

858d7b0 [Cheng Hao] update the typo

This looks like a simple typo ```SparkContext.newHadoopRDD``` instead of ```SparkContext.newAPIHadoopRDD``` as in actual http://spark.apache.org/docs/1.2.1/api/scala/index.html#org.apache.spark.SparkContext

Author: Alexander <abezzubov@nflabs.com>

Closes #4718 from bzz/hadoop-InputFormats-doc-fix and squashes the following commits:

680a4c4 [Alexander] Fix typo in docs on custom Hadoop InputFormats

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

Closes #3490 (close requested by 'andrewor14')
Closes #4646 (close requested by 'srowen')
Closes #3591 (close requested by 'andrewor14')
Closes #3656 (close requested by 'andrewor14')
Closes #4553 (close requested by 'JoshRosen')
Closes #4202 (close requested by 'srowen')
Closes #4497 (close requested by 'marmbrus')
Closes #4150 (close requested by 'andrewor14')
Closes #2409 (close requested by 'andrewor14')
Closes #4221 (close requested by 'srowen')

Fix a overflow bug in JdbcRDD when calculating partitions for large BIGINT ids

Author: Evan Yu <ehotou@gmail.com>

Closes #4701 from hotou/SPARK-5860 and squashes the following commits:

9e038d1 [Evan Yu] [SPARK-5860][CORE] Prevent overflowing at the length level
7883ad9 [Evan Yu] [SPARK-5860][CORE] Prevent overflowing at the length level
c88755a [Evan Yu] [SPARK-5860][CORE] switch to BigInt instead of BigDecimal
4e9ff4f [Evan Yu] [SPARK-5860][CORE] JdbcRDD overflow on large range with high number of partitions

...ests.

Without this SparkHadoopUtil is used by the Client instead of YarnSparkHadoopUtil.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #4711 from harishreedharan/SPARK-5937 and squashes the following commits:

d154de6 [Hari Shreedharan] Use System.clearProperty() instead of setting the value of SPARK_YARN_MODE to empty string.
f729f70 [Hari Shreedharan] Fix ClientSuite to set YARN mode, so that the correct class is used in tests.

Continue to see IllegalStateException in YARN cluster mode. Adding a simple workaround for now.

Author: Nishkam Ravi <nravi@cloudera.com>
Author: nishkamravi2 <nishkamravi@gmail.com>
Author: nravi <nravi@c1704.halxg.cloudera.com>

Closes #4690 from nishkamravi2/master_nravi and squashes the following commits:

d453197 [nishkamravi2] Update NewHadoopRDD.scala
6f41a1d [nishkamravi2] Update NewHadoopRDD.scala
0ce2c32 [nishkamravi2] Update HadoopRDD.scala
f7e33c2 [Nishkam Ravi] Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ba1eb8b [Nishkam Ravi] Try-catch block around the two occurrences of removeShutDownHook. Deletion of semi-redundant occurrences of expensive operation inShutDown.
71d0e17 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
494d8c0 [nishkamravi2] Update DiskBlockManager.scala
3c5ddba [nishkamravi2] Update DiskBlockManager.scala
f0d12de [Nishkam Ravi] Workaround for IllegalStateException caused by recent changes to BlockManager.stop
79ea8b4 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
b446edc [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
5c9a4cb [nishkamravi2] Update TaskSetManagerSuite.scala
535295a [nishkamravi2] Update TaskSetManager.scala
3e1b616 [Nishkam Ravi] Modify test for maxResultSize
9f6583e [Nishkam Ravi] Changes to maxResultSize code (improve error message and add condition to check if maxResultSize > 0)
5f8f9ed [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
636a9ff [nishkamravi2] Update YarnAllocator.scala
8f76c8b [Nishkam Ravi] Doc change for yarn memory overhead
35daa64 [Nishkam Ravi] Slight change in the doc for yarn memory overhead
5ac2ec1 [Nishkam Ravi] Remove out
dac1047 [Nishkam Ravi] Additional documentation for yarn memory overhead issue
42c2c3d [Nishkam Ravi] Additional changes for yarn memory overhead issue
362da5e [Nishkam Ravi] Additional changes for yarn memory overhead
c726bd9 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
f00fa31 [Nishkam Ravi] Improving logging for AM memoryOverhead
1cf2d1e [nishkamravi2] Update YarnAllocator.scala
ebcde10 [Nishkam Ravi] Modify default YARN memory_overhead-- from an additive constant to a multiplier (redone to resolve merge conflicts)
2e69f11 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
efd688a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark
2b630f9 [nravi] Accept memory input as "30g", "512M" instead of an int value, to be consistent with rest of Spark
3bf8fad [nravi] Merge branch 'master' of https://github.com/apache/spark
5423a03 [nravi] Merge branch 'master' of https://github.com/apache/spark
eb663ca [nravi] Merge branch 'master' of https://github.com/apache/spark
df2aeb1 [nravi] Improved fix for ConcurrentModificationIssue (Spark-1097, Hadoop-10456)
6b840f0 [nravi] Undo the fix for SPARK-1758 (the problem is fixed)
5108700 [nravi] Fix in Spark for the Concurrent thread modification issue (SPARK-1097, HADOOP-10456)
681b36f [nravi] Fix for SPARK-1758: failing test org.apache.spark.JavaAPISuite.wholeTextFiles

fix typo: it should be "default:" instead of "default;"

Author: Jacky Li <jackylk@users.noreply.github.com>

Closes #4713 from jackylk/patch-10 and squashes the following commits:

15daf2e [Jacky Li] [MLlib] fix typo

Fix createDataFrame() from pandas DataFrame (not tested by jenkins, depends on SPARK-5693).

It also support to create DataFrame from plain tuple/list without column names, `_1`, `_2` will be used as column names.

Author: Davies Liu <davies@databricks.com>

Closes #4679 from davies/pandas and squashes the following commits:

c0cbe0b [Davies Liu] fix tests
8466d1d [Davies Liu] fix create DataFrame from pandas

For SPARK-5867:
* The spark.ml programming guide needs to be updated to use the new SQL DataFrame API instead of the old SchemaRDD API.
* It should also include Python examples now.

For SPARK-5892:
* Fix Python docs
* Various other cleanups

BTW, I accidentally merged this with master.  If you want to compile it on your own, use this branch which is based on spark/branch-1.3 and cherry-picks the commits from this PR: [https://github.com/jkbradley/spark/tree/doc-review-1.3-check]

CC: mengxr  (ML),  davies  (Python docs)

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4675 from jkbradley/doc-review-1.3 and squashes the following commits:

f191bb0 [Joseph K. Bradley] small cleanups
e786efa [Joseph K. Bradley] small doc corrections
6b1ab4a [Joseph K. Bradley] fixed python lint test
946affa [Joseph K. Bradley] Added sample data for ml.MovieLensALS example.  Changed spark.ml Java examples to use DataFrames API instead of sql()
da81558 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into doc-review-1.3
629dbf5 [Joseph K. Bradley] Updated based on code review: * made new page for old migration guides * small fixes * moved inherit_doc in python
b9df7c4 [Joseph K. Bradley] Small cleanups: toDF to toDF(), adding s for string interpolation
34b067f [Joseph K. Bradley] small doc correction
da16aef [Joseph K. Bradley] Fixed python mllib docs
8cce91c [Joseph K. Bradley] GMM: removed old imports, added some doc
695f3f6 [Joseph K. Bradley] partly done trying to fix inherit_doc for class hierarchies in python docs
a72c018 [Joseph K. Bradley] made ChiSqTestResult appear in python docs
b05a80d [Joseph K. Bradley] organize imports. doc cleanups
e572827 [Joseph K. Bradley] updated programming guide for ml and mllib

Follow-on to https://github.com/apache/spark/pull/4591

Document isEmpty / take / parallelize and their interaction with (an empty) RDD[Nothing] and RDD[Null]. Also, fix a marginally related minor issue with histogram() and EmptyRDD.

CC rxin since you reviewed the last one although I imagine this is an uncontroversial resolution.

Author: Sean Owen <sowen@cloudera.com>

Closes #4698 from srowen/SPARK-5744.2 and squashes the following commits:

9b2a811 [Sean Owen] 2 extra javadoc fixes
d1b9fba [Sean Owen] Document isEmpty / take / parallelize and their interaction with (an empty) RDD[Nothing] and RDD[Null]. Also, fix a marginally related minor issue with histogram() and EmptyRDD.

JIRA: https://issues.apache.org/jira/browse/SPARK-5909

Author: Yin Huai <yhuai@databricks.com>

Closes #4694 from yhuai/clearCache and squashes the following commits:

397ecc4 [Yin Huai] Address comments.
a2702fc [Yin Huai] Update parser.
3a54506 [Yin Huai] add isEmpty to CacheManager.
6d14460 [Yin Huai] Python clearCache.
f7b8dbd [Yin Huai] Add clear cache command.

In the general case, Spillable's heuristic of checking for memory stress
on every 32nd item after 1000 items are read is good enough. In general,
we do not want to be enacting the spilling checks until later on in the
job; checking for disk-spilling too early can produce unacceptable
performance impact in trivial cases.

However, there are non-trivial cases, particularly if each serialized
object is large, where checking for the necessity to spill too late
would allow the memory to overflow. Consider if every item is 1.5 MB in
size, and the heap size is 1000 MB. Then clearly if we only try to spill
the in-memory contents to disk after 1000 items are read, we would have
already accumulated 1500 MB of RAM and overflowed the heap.

Patch #3656 attempted to circumvent this by checking the need to spill
on every single item read, but that would cause unacceptable performance
in the general case. However, the convoluted cases above should not be
forced to be refactored to shrink the data items. Therefore it makes
sense that the memory spilling thresholds be configurable.

Author: mcheah <mcheah@palantir.com>

Closes #4420 from mingyukim/memory-spill-configurable and squashes the following commits:

6e2509f [mcheah] [SPARK-4808] Removing minimum number of elements read before spill check

In the previous version, PIC stores clustering assignments as an `RDD[(Long, Int)]`. This is mapped to `RDD<Tuple2<Object, Object>>` in Java and hence Java users have to cast types manually. We should either create a new method called `javaAssignments` that returns `JavaRDD[(java.lang.Long, java.lang.Int)]` or wrap the result pair in a class. I chose the latter approach in this PR. Now assignments are stored as an `RDD[Assignment]`, where `Assignment` is a class with `id` and `cluster`.

Similarly, in FPGrowth, the frequent itemsets are stored as an `RDD[(Array[Item], Long)]`, which is mapped to `RDD<Tuple2<Object, Object>>`. Though we provide a "Java-friendly" method `javaFreqItemsets` that returns `JavaRDD[(Array[Item], java.lang.Long)]`. It doesn't really work because `Array[Item]` is mapped to `Object` in Java. So in this PR I created a class `FreqItemset` to wrap the results. It has `items` and `freq`, as well as a `javaItems` method that returns `List<Item>` in Java.

I'm not certain that the names I chose are proper: `Assignment`/`id`/`cluster` and `FreqItemset`/`items`/`freq`. Please let me know if there are better suggestions.

CC: jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #4695 from mengxr/SPARK-5900 and squashes the following commits:

865b5ca [Xiangrui Meng] make Assignment serializable
cffa96e [Xiangrui Meng] fix test
9c0e590 [Xiangrui Meng] remove unused Tuple2
1b9db3d [Xiangrui Meng] make PIC and FPGrowth Java-friendly

I've updated documentation to reflect true behavior of this setting in client vs. cluster mode.

Author: Ilya Ganelin <ilya.ganelin@capitalone.com>

Closes #4665 from ilganeli/SPARK-5570 and squashes the following commits:

5d1c8dd [Ilya Ganelin] Added example configuration code
a51700a [Ilya Ganelin] Getting rid of extra spaces
85f7a08 [Ilya Ganelin] Reworded note
5889d43 [Ilya Ganelin] Formatting adjustment
f149ba1 [Ilya Ganelin] Minor updates
1fec7a5 [Ilya Ganelin] Updated to add clarification for other driver properties
db47595 [Ilya Ganelin] Slight formatting update
c899564 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5570
17b751d [Ilya Ganelin] Updated documentation for driver-memory to reflect its true behavior in client vs cluster mode

Another one from JoshRosen 's wish list. The first commit is much smaller and removes 2 of the 4 Clock classes. The second is much larger, necessary for consolidating the streaming one. I put together implementations in the way that seemed simplest. Almost all the change is standardizing class and method names.

Author: Sean Owen <sowen@cloudera.com>

Closes #4514 from srowen/SPARK-4682 and squashes the following commits:

5ed3a03 [Sean Owen] Javadoc Clock classes; make ManualClock private[spark]
169dd13 [Sean Owen] Add support for legacy org.apache.spark.streaming clock class names
277785a [Sean Owen] Reduce the net change in this patch by reversing some unnecessary syntax changes along the way
b5e53df [Sean Owen] FakeClock -> ManualClock; getTime() -> getTimeMillis()
160863a [Sean Owen] Consolidate Streaming Clock class into common util Clock
7c956b2 [Sean Owen] Consolidate Clocks except for Streaming Clock

Currently the pid file is not deleted, and potentially may cause some problem after service is stopped. The fix remove the pid file after service stopped.

Author: Zhan Zhang <zhazhan@gmail.com>

Closes #4676 from zhzhan/spark-5889 and squashes the following commits:

eb01be1 [Zhan Zhang] solve review comments
b4c009e [Zhan Zhang] solve review comments
018110a [Zhan Zhang] spark-5889: remove pid file after stopping service
088d2a2 [Zhan Zhang] squash all commits
c1f1fa5 [Zhan Zhang] test

For users to implement their own PipelineStages, we need to make PipelineStage.transformSchema be public instead of private to ml.  This would be nice to include in Spark 1.3

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4682 from jkbradley/SPARK-5902 and squashes the following commits:

6f02357 [Joseph K. Bradley] Made transformSchema public
0e6d0a0 [Joseph K. Bradley] made implementations of transformSchema protected as well
fdaf26a [Joseph K. Bradley] Made PipelineStage.transformSchema protected instead of private[ml]