Both akka 2.3.x and hadoop-2.x use protobuf 2.5 so only hadoop-1 build needs
custom 2.3.4-spark akka version that shades protobuf-2.5

This partially fixes SPARK-7042 (for hadoop-2.x builds)

Author: Konstantin Shaposhnikov <Konstantin.Shaposhnikov@sc.com>

Closes #6341 from kostya-sh/SPARK-7042 and squashes the following commits:

7eb8c60 [Konstantin Shaposhnikov] [SPARK-7042][BUILD] use the standard akka artifacts with hadoop-2.x

The Catalyst DSL is no longer used as a public facing API. This pull request removes the UDF and writeToFile feature from it since they are not used in unit tests.

Author: Reynold Xin <rxin@databricks.com>

Closes #6350 from rxin/unused-logical-dsl and squashes the following commits:

90b3de6 [Reynold Xin] [SQL][minor] Removed unused Catalyst logical plan DSL.

https://issues.apache.org/jira/browse/SPARK-7832

Author: Yin Huai <yhuai@databricks.com>

Closes #6385 from yhuai/runSQLTests and squashes the following commits:

3d399bc [Yin Huai] Always run SQL tests in master build.

Adds a section in the RDD persistence section of the programming-guide docs detailing Spark-Tachyon version compatibility as discussed in [[SPARK-6391]](https://issues.apache.org/jira/browse/SPARK-6391).

Author: Calvin Jia <jia.calvin@gmail.com>

Closes #6382 from calvinjia/spark-6391 and squashes the following commits:

113e863 [Calvin Jia] Move compatibility info to the offheap storage level section.
7942dc5 [Calvin Jia] Add a section in the programming-guide docs for Tachyon compatibility.

When committing/aborting a write task issued in `InsertIntoHadoopFsRelation`, if an exception is thrown from `OutputWriter.close()`, the committing/aborting process will be interrupted, and leaves messy stuff behind (e.g., the `_temporary` directory created by `FileOutputCommitter`).

This PR makes these two process more robust by catching potential exceptions and falling back to normal task committment/abort.

Author: Cheng Lian <lian@databricks.com>

Closes #6378 from liancheng/spark-7838 and squashes the following commits:

f18253a [Cheng Lian] Makes task committing/aborting in InsertIntoHadoopFsRelation more robust

[SPARK-7684] [SQL] Invoking HiveContext.newTemporaryConfiguration() shouldn't create new metastore directory

The "Database does not exist" error reported in SPARK-7684 was caused by `HiveContext.newTemporaryConfiguration()`, which always creates a new temporary metastore directory and returns a metastore configuration pointing that directory. This makes `TestHive.reset()` always replaces old temporary metastore with an empty new one.

Author: Cheng Lian <lian@databricks.com>

Closes #6359 from liancheng/spark-7684 and squashes the following commits:

95d2eb8 [Cheng Lian] Addresses @marmbrust's comment
042769d [Cheng Lian] Don't create new temp directory in HiveContext.newTemporaryConfiguration()

This PR adds test which shows that Kryo buffer size configured in mb is supported properly

Author: tedyu <yuzhihong@gmail.com>

Closes #6390 from tedyu/master and squashes the following commits:

c51ea64 [tedyu] Fix KryoSerializer creation
f12ee04 [tedyu] Correct conf variable name in test
642de51 [tedyu] Drop change in KryoSerializer so that the new test runs
d2fdbc4 [tedyu] Give bufferSizeKb initial value
9a17277 [tedyu] Rewrite bufferSize checking
4739998 [tedyu] Rewrite bufferSize checking
830d0d0 [tedyu] Kryo buffer size configured in mb should be properly supported

Author: tedyu <yuzhihong@gmail.com>

Closes #6381 from ted-yu/master and squashes the following commits:

e2f0ea1 [tedyu] Close HBaseAdmin at the end of HBaseTest

Fix minor typo on metrics.properties.template where slf4j is incorrectly spelled as sl4j.

Author: Judy Nash <judynash@microsoft.com>

Closes #6362 from judynash/master and squashes the following commits:

c644875 [Judy Nash] SPARK-7811: Fix typo on slf4j configuration on metrics.properties.template

Author: Ram Sriharsha <rsriharsha@hw11853.local>

Closes #6365 from harsha2010/SPARK-7833 and squashes the following commits:

923f288 [Ram Sriharsha] cleanup
7623b7d [Ram Sriharsha] python style fix
9743f83 [Ram Sriharsha] [SPARK-7833][ml] Add python wrapper for RegressionEvaluator

https://issues.apache.org/jira/browse/SPARK-7805

Because `sql/hive`'s tests depend on the test jar of `sql/core`, we do not need to store `SQLTestUtils` and `ParquetTest` in `src/main`. We should only add stuff that will be needed by `sql/console` or Python tests (for Python, we need it in `src/main`, right? davies).

Author: Yin Huai <yhuai@databricks.com>

Closes #6334 from yhuai/SPARK-7805 and squashes the following commits:

af6d0c9 [Yin Huai] mima
b86746a [Yin Huai] Move SQLTestUtils.scala and ParquetTest.scala to src/test.

https://issues.apache.org/jira/browse/SPARK-7845

Author: Yin Huai <yhuai@databricks.com>

Closes #6384 from yhuai/hadoop1Test and squashes the following commits:

82fcea8 [Yin Huai] Use hadoop 1.2.1 (a stable version) for hadoop 1 test.

This is to fix an issue reported in #6373 where the `cp` would fail if `-Psparkr` was not used in the build

cc dragos pwendell

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

Closes #6379 from shivaram/make-distribution-hotfix and squashes the following commits:

08eb7e4 [Shivaram Venkataraman] Copy SparkR lib if it exists in make-distribution

This one continues the work of https://github.com/apache/spark/pull/6216.

Author: Yin Huai <yhuai@databricks.com>
Author: Reynold Xin <rxin@databricks.com>

Closes #6366 from yhuai/insert and squashes the following commits:

3d717fb [Yin Huai] Use insertInto to handle the casue when table exists and Append is used for saveAsTable.
56d2540 [Yin Huai] Add PreWriteCheck to HiveContext's analyzer.
c636e35 [Yin Huai] Remove unnecessary empty lines.
cf83837 [Yin Huai] Move insertInto to write. Also, remove the partition columns from InsertIntoHadoopFsRelation.
0841a54 [Reynold Xin] Removed experimental tag for deprecated methods.
33ed8ef [Reynold Xin] [SPARK-7654][SQL] Move insertInto into reader/writer interface.

jira-pytyhon package should be installed by

  sudo pip install jira

cc pwendell

Author: Davies Liu <davies@databricks.com>

Closes #6367 from davies/fix_jira_python2 and squashes the following commits:

fbb3c8e [Davies Liu] Fix install jira-python

Add tests later.

Author: Davies Liu <davies@databricks.com>

Closes #6375 from davies/insertInto and squashes the following commits:

826423e [Davies Liu] add insertInto() to Writer

1. ntile should take an integer as parameter.
2. Added Python API (based on #6364)
3. Update documentation of various DataFrame Python functions.

Author: Davies Liu <davies@databricks.com>
Author: Reynold Xin <rxin@databricks.com>

Closes #6374 from rxin/window-final and squashes the following commits:

69004c7 [Reynold Xin] Style fix.
288cea9 [Reynold Xin] Update documentaiton.
7cb8985 [Reynold Xin] Merge pull request #6364 from davies/window
66092b4 [Davies Liu] update docs
ed73cb4 [Reynold Xin] [SPARK-7322][SQL] Improve DataFrame window function documentation.
ef55132 [Davies Liu] Merge branch 'master' of github.com:apache/spark into window4
8936ade [Davies Liu] fix maxint in python 3
2649358 [Davies Liu] update docs
778e2c0 [Davies Liu] SPARK-7836 and SPARK-7822: Python API of window functions

In the old implementation, if a batch has no block, `areWALRecordHandlesPresent` will be `true` and it will return `WriteAheadLogBackedBlockRDD`.

This PR handles this case by returning `WriteAheadLogBackedBlockRDD` or `BlockRDD` according to the configuration.

Author: zsxwing <zsxwing@gmail.com>

Closes #6372 from zsxwing/SPARK-7777 and squashes the following commits:

788f895 [zsxwing] Handle the case when there is no block in a batch

This change also remove native libraries from SparkR to make sure our distribution works across platforms

Tested by building on Mac, running on Amazon Linux (CentOS), Windows VM and vice-versa (built on Linux run on Mac)

I will also test this with YARN soon and update this PR.

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

Closes #6373 from shivaram/sparkr-binary and squashes the following commits:

ae41b5c [Shivaram Venkataraman] Remove native libraries from SparkR Also include the built SparkR package in make-distribution.sh

sqlCtx -> sqlContext

You can check the docs by:

```
$ cd docs
$ SKIP_SCALADOC=1 jekyll serve
```
cc shivaram

Author: Davies Liu <davies@databricks.com>

Closes #5442 from davies/r_docs and squashes the following commits:

7a12ec6 [Davies Liu] remove rdd in R docs
8496b26 [Davies Liu] remove the docs related to RDD
e23b9d6 [Davies Liu] delete R docs for RDD API
222e4ff [Davies Liu] Merge branch 'master' into r_docs
89684ce [Davies Liu] Merge branch 'r_docs' of github.com:davies/spark into r_docs
f0a10e1 [Davies Liu] address comments from @shivaram
f61de71 [Davies Liu] Update pairRDD.R
3ef7cf3 [Davies Liu] use + instead of function(a,b) a+b
2f10a77 [Davies Liu] address comments from @cafreeman
9c2a062 [Davies Liu] mention R api together with Python API
23f751a [Davies Liu] Fill in SparkR examples in programming guide

Hi,

Following the discussion in http://apache-spark-developers-list.1001551.n3.nabble.com/python-converter-in-HBaseConverter-scala-spark-examples-td10001.html. I made some modification in three files in package examples:
1. HBaseConverters.scala: the new converter will converts all the records in an hbase results into a single string
2. hbase_input.py: as the value string may contain several records, we can use ast package to convert the string into dict
3. HBaseTest.scala: as the package examples use hbase 0.98.7 the original constructor HTableDescriptor is deprecated. The updation to new constructor is made

Author: GenTang <gen.tang86@gmail.com>

Closes #3920 from GenTang/master and squashes the following commits:

d2153df [GenTang] import JSONObject precisely
4802481 [GenTang] dump the result into a singl String
62df7f0 [GenTang] remove the comment
21de653 [GenTang] return the string in json format
15b1fe3 [GenTang] the modification of comments
5cbbcfc [GenTang] the improvement of pythonconverter
ceb31c5 [GenTang] the modification for adapting updation of hbase
3253b61 [GenTang] the modification accompanying the improvement of pythonconverter

#6166 added the driver logs to `SparkListenerApplicationStart`. This  adds tests in `JsonProtocolSuite` to ensure we don't regress.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #6368 from harishreedharan/jsonprotocol-test and squashes the following commits:

dc9eafc [Hari Shreedharan] [HOTFIX] Add tests for SparkListenerApplicationStart with Driver Logs.

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

Closes #6369 from tdas/SPARK-7838 and squashes the following commits:

87d1c7f [Tathagata Das] Addressed comment
37775d8 [Tathagata Das] set scope for kinesis stream

Enables the SparkR profiles for all the binary builds we create

cc pwendell

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

Closes #6371 from shivaram/sparkr-create-release and squashes the following commits:

ca5a0b2 [Shivaram Venkataraman] Add -Psparkr to create-release.sh

My experiments with scheduling very short tasks in standalone cluster mode indicated that a significant amount of time was being spent in scheduling the tasks (>500ms for 256 tasks).  I found that most of the time was being spent in creating a new instance of serializer for each task.  Changing this to just one serializer brought down the scheduling time to 8ms.

Author: Akshat Aranya <aaranya@quantcast.com>

Closes #6323 from coolfrood/master and squashes the following commits:

12d8c9e [Akshat Aranya] Reduce visibility of serializer
bd4a5dd [Akshat Aranya] Style fix
0b8ca93 [Akshat Aranya] Incorporate review comments
fe530cd [Akshat Aranya] Speed up task scheduling in standalone mode by reusing serializer instead of creating a new one for each task.

[SPARK-7830] [DOCS] [MLLIB] Adding logistic regression to the list of Multiclass Classification Supported Methods documentation

Added logistic regression to the list of Multiclass Classification Supported Methods in the MLlib Classification and Regression documentation, as it was missing.

Author: Mike Dusenberry <dusenberrymw@gmail.com>

Closes #6357 from dusenberrymw/Add_LR_To_List_Of_Multiclass_Classification_Methods and squashes the following commits:

7918650 [Mike Dusenberry] Updating broken link due to the "Binary Classification" section on the Linear Methods page being renamed to "Classification".
3005dc2 [Mike Dusenberry] Adding logistic regression to the list of Multiclass Classification Supported Methods in the MLlib Classification and Regression documentation, as it was missing.

The previous PR for SPARK-7224 (#5790) broke JDK 6, because it used java.nio.Path, which was in jdk 7, and not in 6. This PR uses Guava's `Files` to handle directory creation, and etc...

The description from the previous PR:
> This patch contains an `IvyTestUtils` file, which dynamically generates jars and pom files to test the `--packages` feature without having to rely on the internet, and Maven Central.

cc pwendell

I also rand the flaky test about 20 times locally, it didn't fail a single time, but I think it may fail like once every 100 builds? I still haven't figured the cause yet, but the test before it, `--jars` was also failing after we turned off the `--packages` test in `SparkSubmitSuite`. It may be related to the launch of SparkSubmit.

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5892 from brkyvz/maven-utils and squashes the following commits:

e9b1903 [Burak Yavuz] fix merge conflict
68214e0 [Burak Yavuz] remove ignore for test(neglect spark dependencies)
e632381 [Burak Yavuz] fix ignore
9ef1408 [Burak Yavuz] re-enable --packages test
22eea62 [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into maven-utils
05cd0de [Burak Yavuz] added mock repository generator

KinesisReceiver calls worker.run() which is a blocking call (while loop) as per source code of kinesis-client library - https://github.com/awslabs/amazon-kinesis-client/blob/v1.2.1/src/main/java/com/amazonaws/services/kinesis/clientlibrary/lib/worker/Worker.java.
This results in infinite loop while calling sparkStreamingContext.stop(stopSparkContext = false, stopGracefully = true) perhaps because ReceiverTracker is never able to register the receiver (it's receiverInfo field is a empty map) causing it to be stuck in infinite loop while waiting for running flag to be set to false.

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

Closes #6348 from tdas/SPARK-7788 and squashes the following commits:

2584683 [Tathagata Das] Added receiver id in thread name
6cf1cd4 [Tathagata Das] Made KinesisReceiver.onStart non-blocking

The default add time of 5s is still too slow for small jobs. Also, the current default remove time of 10 minutes seem rather high. This patch lowers both and rephrases a few log messages.

Author: Andrew Or <andrew@databricks.com>

Closes #6301 from andrewor14/da-minor and squashes the following commits:

6d614a6 [Andrew Or] Lower log level
2811492 [Andrew Or] Log information when requests are canceled
5fcd3eb [Andrew Or] Fix tests
3320710 [Andrew Or] Lower timeouts + rephrase a few log messages

Author: Michael Armbrust <michael@databricks.com>

Closes #6363 from marmbrus/windowErrors and squashes the following commits:

516b02d [Michael Armbrust] [SPARK-7834] [SQL] Better window error messages

Author: Imran Rashid <irashid@cloudera.com>

Closes #6284 from squito/SPARK-7760 and squashes the following commits:

5e02d8a [Imran Rashid] style; increase timeout
9987399 [Imran Rashid] comment
8c7ed63 [Imran Rashid] add /json back into master & worker pages; add test

JIRA: https://issues.apache.org/jira/browse/SPARK-7270

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #5864 from viirya/dyn_partition_insert and squashes the following commits:

b5627df [Liang-Chi Hsieh] For comments.
3b21e4b [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into dyn_partition_insert
8a4352d [Liang-Chi Hsieh] Consider dynamic partition when inserting into hive table.

Author: Santiago M. Mola <santi@mola.io>

Closes #6327 from smola/feature/catalyst-dsl-set-ops and squashes the following commits:

11db778 [Santiago M. Mola] [SPARK-7724] [SQL] Support Intersect/Except in Catalyst DSL.

https://issues.apache.org/jira/browse/SPARK-7758

When initializing `executionHive`, we only masks
`javax.jdo.option.ConnectionURL` to override metastore location.  However,
other properties that relates to the actual Hive metastore data source are not
masked.  For example, when using Spark SQL with a PostgreSQL backed Hive
metastore, `executionHive` actually tries to use settings read from
`hive-site.xml`, which talks about PostgreSQL, to connect to the temporary
Derby metastore, thus causes error.

To fix this, we need to mask all metastore data source properties.
Specifically, according to the code of [Hive `ObjectStore.getDataSourceProps()`
method] [1], all properties whose name mentions "jdo" and "datanucleus" must be
included.

[1]: https://github.com/apache/hive/blob/release-0.13.1/metastore/src/java/org/apache/hadoop/hive/metastore/ObjectStore.java#L288

Have tested using postgre sql as metastore, it worked fine.

Author: WangTaoTheTonic <wangtao111@huawei.com>

Closes #6314 from WangTaoTheTonic/SPARK-7758 and squashes the following commits:

ca7ae7c [WangTaoTheTonic] add comments
86caf2c [WangTaoTheTonic] delete unused import
e4f0feb [WangTaoTheTonic] block more data source related property
92a81fa [WangTaoTheTonic] fix style check
e3e683d [WangTaoTheTonic] override more configs to avoid failuer connecting to postgre sql

SPARK-3386 / #5606 modified the shuffle write path to re-use serializer instances across multiple calls to DiskBlockObjectWriter. It turns out that this introduced a very rare bug when using `KryoSerializer`: if auto-reset is disabled and reference-tracking is enabled, then we'll end up re-using the same serializer instance to write multiple output streams without calling `reset()` between write calls, which can lead to cases where objects in one file may contain references to objects that are in previous files, causing errors during deserialization.

This patch fixes this bug by calling `reset()` at the start of `serialize()` and `serializeStream()`. I also added a regression test which demonstrates that this problem only occurs when auto-reset is disabled and reference-tracking is enabled.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6293 from JoshRosen/kryo-instance-reuse-bug and squashes the following commits:

e19726d [Josh Rosen] Add fix for SPARK-7766.
71845e3 [Josh Rosen] Add failing regression test to trigger Kryo re-use bug

Including Iris Dataset (after shuffling and relabeling 3 -> 0 to confirm to 0 -> numClasses-1 labeling). Could not find an existing dataset in data/mllib for multiclass classification.

Author: Ram Sriharsha <rsriharsha@hw11853.local>

Closes #6296 from harsha2010/SPARK-7574 and squashes the following commits:

645427c [Ram Sriharsha] cleanup
46c41b1 [Ram Sriharsha] cleanup
2f76295 [Ram Sriharsha] Code Review Fixes
ebdf103 [Ram Sriharsha] Java Example
c026613 [Ram Sriharsha] Code Review fixes
4b7d1a6 [Ram Sriharsha] minor cleanup
13bed9c [Ram Sriharsha] add wikipedia link
bb9dbfa [Ram Sriharsha] Clean up naming
6f90db1 [Ram Sriharsha] [SPARK-7574][ml][doc] User guide for OneVsRest

This reverts commit 147b6be3.

Author: Ram Sriharsha <rsriharsha@hw11853.local>

Closes #6344 from harsha2010/SPARK-7404 and squashes the following commits:

16b9d77 [Ram Sriharsha] consistent naming
7f100b6 [Ram Sriharsha] cleanup
c46044d [Ram Sriharsha] Merge with Master + Code Review Fixes
188fa0a [Ram Sriharsha] Merge branch 'master' into SPARK-7404
f5b6a4c [Ram Sriharsha] cleanup doc
97beca5 [Ram Sriharsha] update test to use R packages
32dd310 [Ram Sriharsha] fix indentation
f93b812 [Ram Sriharsha] fix test
1b6ebb3 [Ram Sriharsha] [SPARK-7404][ml] Add RegressionEvaluator to spark.ml

Author: Michael Armbrust <michael@databricks.com>

Closes #6165 from marmbrus/wrongColumn and squashes the following commits:

4fad158 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into wrongColumn
aad7eab [Michael Armbrust] rxins comments
f1e8df1 [Michael Armbrust] [SPARK-6743][SQL] Fix empty projections of cached data