## What changes were proposed in this pull request?
Integrate Apache Arrow with Spark to increase performance of `DataFrame.toPandas`.  This has been done by using Arrow to convert data partitions on the executor JVM to Arrow payload byte arrays where they are then served to the Python process.  The Python DataFrame can then collect the Arrow payloads where they are combined and converted to a Pandas DataFrame.  All non-complex data types are currently supported, otherwise an `UnsupportedOperation` exception is thrown.

Additions to Spark include a Scala package private method `Dataset.toArrowPayloadBytes` that will convert data partitions in the executor JVM to `ArrowPayload`s as byte arrays so they can be easily served.  A package private class/object `ArrowConverters` that provide data type mappings and conversion routines.  In Python, a public method `DataFrame.collectAsArrow` is added to collect Arrow payloads and an optional flag in `toPandas(useArrow=False)` to enable using Arrow (uses the old conversion by default).

## How was this patch tested?
Added a new test suite `ArrowConvertersSuite` that will run tests on conversion of Datasets to Arrow payloads for supported types.  The suite will generate a Dataset and matching Arrow JSON data, then the dataset is converted to an Arrow payload and finally validated against the JSON data.  This will ensure that the schema and data has been converted correctly.

Added PySpark tests to verify the `toPandas` method is producing equal DataFrames with and without pyarrow.  A roundtrip test to ensure the pandas DataFrame produced by pyspark is equal to a one made directly with pandas.

Author: Bryan Cutler <cutlerb@gmail.com>
Author: Li Jin <ice.xelloss@gmail.com>
Author: Li Jin <li.jin@twosigma.com>
Author: Wes McKinney <wes.mckinney@twosigma.com>

Closes #15821 from BryanCutler/wip-toPandas_with_arrow-SPARK-13534.

## What changes were proposed in this pull request?

Update hadoop-2.7 profile's curator version to 2.7.1, more see [SPARK-13933](https://issues.apache.org/jira/browse/SPARK-13933).

## How was this patch tested?

manual tests

Author: Yuming Wang <wgyumg@gmail.com>

Closes #18247 from wangyum/SPARK-13933.

This change adds an abstraction and LevelDB implementation for a key-value
store that will be used to store UI and SHS data.

The interface is described in KVStore.java (see javadoc). Specifics
of the LevelDB implementation are discussed in the javadocs of both
LevelDB.java and LevelDBTypeInfo.java.

Included also are a few small benchmarks just to get some idea of
latency. Because they're too slow for regular unit test runs, they're
disabled by default.

Tested with the included unit tests, and also as part of the overall feature
implementation (including running SHS with hundreds of apps).

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #17902 from vanzin/shs-ng/M1.

## What changes were proposed in this pull request?

Add a new `spark-hadoop-cloud` module and maven profile to pull in object store support from `hadoop-openstack`, `hadoop-aws` and `hadoop-azure` (Hadoop 2.7+) JARs, along with their dependencies, fixing up the dependencies so that everything works, in particular Jackson.

It restores `s3n://` access to S3, adds its `s3a://` replacement, OpenStack `swift://` and azure `wasb://`.

There's a documentation page, `cloud_integration.md`, which covers the basic details of using Spark with object stores, referring the reader to the supplier's own documentation, with specific warnings on security and the possible mismatch between a store's behavior and that of a filesystem. In particular, users are advised be very cautious when trying to use an object store as the destination of data, and to consult the documentation of the storage supplier and the connector.

(this is the successor to #12004; I can't re-open it)

## How was this patch tested?

Downstream tests exist in [https://github.com/steveloughran/spark-cloud-examples/tree/master/cloud-examples](https://github.com/steveloughran/spark-cloud-examples/tree/master/cloud-examples)

Those verify that the dependencies are sufficient to allow downstream applications to work with s3a, azure wasb and swift storage connectors, and perform basic IO & dataframe operations thereon. All seems well.

Manually clean build & verify that assembly contains the relevant aws-* hadoop-* artifacts on Hadoop 2.6; azure on a hadoop-2.7 profile.

SBT build: `build/sbt -Phadoop-cloud -Phadoop-2.7 package`
maven build `mvn install -Phadoop-cloud -Phadoop-2.7`

This PR *does not* update `dev/deps/spark-deps-hadoop-2.7` or `dev/deps/spark-deps-hadoop-2.6`, because unless the hadoop-cloud profile is enabled, no extra JARs show up in the dependency list. The dependency check in Jenkins isn't setting the property, so the new JARs aren't visible.

Author: Steve Loughran <stevel@apache.org>
Author: Steve Loughran <stevel@hortonworks.com>

Closes #17834 from steveloughran/cloud/SPARK-7481-current.

## What changes were proposed in this pull request?

Fix build warnings primarily related to Breeze 0.13 operator changes, Java style problems

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #17803 from srowen/SPARK-20523.

Upgrade Jetty so it can work with Hadoop 3 (alpha 2 release, in particular).
Without this change, because of incompatibily between Jetty versions,
Spark fails to compile when built against Hadoop 3

## How was this patch tested?
Unit tests being run.

Author: Mark Grover <mark@apache.org>

Closes #17790 from markgrover/spark-20514.

## What changes were proposed in this pull request?
Upgrade breeze version to 0.13.1, which fixed some critical bugs of L-BFGS-B.

## How was this patch tested?
Existing unit tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #17746 from yanboliang/spark-20449.

This patch bumps the master branch version to `2.3.0-SNAPSHOT`.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #17753 from JoshRosen/SPARK-20453.

## What changes were proposed in this pull request?

This PR proposes two things as below:

- Avoid Unidoc build only if Hadoop 2.6 is explicitly set in SBT build

  Due to a different dependency resolution in SBT & Unidoc by an unknown reason, the documentation build fails on a specific machine & environment in Jenkins but it was unable to reproduce.

  So, this PR just checks an environment variable `AMPLAB_JENKINS_BUILD_PROFILE` that is set in Hadoop 2.6 SBT build against branches on Jenkins, and then disables Unidoc build. **Note that PR builder will still build it with Hadoop 2.6 & SBT.**

  ```
  ========================================================================
  Building Unidoc API Documentation
  ========================================================================
  [info] Building Spark unidoc (w/Hive 1.2.1) using SBT with these arguments:  -Phadoop-2.6 -Pmesos -Pkinesis-asl -Pyarn -Phive-thriftserver -Phive unidoc
  Using /usr/java/jdk1.8.0_60 as default JAVA_HOME.
  ...
  ```

  I checked the environment variables from the logs (first bit) as below:

  - **spark-master-test-sbt-hadoop-2.6** (this one is being failed) - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-master-test-sbt-hadoop-2.6/lastBuild/consoleFull

  ```
  JAVA_HOME=/usr/java/jdk1.8.0_60
  JAVA_7_HOME=/usr/java/jdk1.7.0_79
  SPARK_BRANCH=master
  AMPLAB_JENKINS_BUILD_PROFILE=hadoop2.6   <- I use this variable
  AMPLAB_JENKINS="true"
  ```
  - spark-master-test-sbt-hadoop-2.7 - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-master-test-sbt-hadoop-2.7/lastBuild/consoleFull

  ```
  JAVA_HOME=/usr/java/jdk1.8.0_60
  JAVA_7_HOME=/usr/java/jdk1.7.0_79
  SPARK_BRANCH=master
  AMPLAB_JENKINS_BUILD_PROFILE=hadoop2.7
  AMPLAB_JENKINS="true"
  ```

  - spark-master-test-maven-hadoop-2.6 - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-master-test-maven-hadoop-2.6/lastBuild/consoleFull

  ```
  JAVA_HOME=/usr/java/jdk1.8.0_60
  JAVA_7_HOME=/usr/java/jdk1.7.0_79
  HADOOP_PROFILE=hadoop-2.6
  HADOOP_VERSION=
  SPARK_BRANCH=master
  AMPLAB_JENKINS="true"
  ```

  - spark-master-test-maven-hadoop-2.7 - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-master-test-maven-hadoop-2.7/lastBuild/consoleFull

  ```
  JAVA_HOME=/usr/java/jdk1.8.0_60
  JAVA_7_HOME=/usr/java/jdk1.7.0_79
  HADOOP_PROFILE=hadoop-2.7
  HADOOP_VERSION=
  SPARK_BRANCH=master
  AMPLAB_JENKINS="true"
  ```

  - PR builder - https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/75843/consoleFull

  ```
  JENKINS_MASTER_HOSTNAME=amp-jenkins-master
  JAVA_HOME=/usr/java/jdk1.8.0_60
  JAVA_7_HOME=/usr/java/jdk1.7.0_79
  ```

  Assuming from other logs in branch-2.1

    - SBT & Hadoop 2.6 against branch-2.1 https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-branch-2.1-test-sbt-hadoop-2.6/lastBuild/consoleFull

      ```
      JAVA_HOME=/usr/java/jdk1.8.0_60
      JAVA_7_HOME=/usr/java/jdk1.7.0_79
      SPARK_BRANCH=branch-2.1
      AMPLAB_JENKINS_BUILD_PROFILE=hadoop2.6
      AMPLAB_JENKINS="true"
      ```

    - Maven & Hadoop 2.6 against branch-2.1 https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-branch-2.1-test-maven-hadoop-2.6/lastBuild/consoleFull

      ```
      JAVA_HOME=/usr/java/jdk1.8.0_60
      JAVA_7_HOME=/usr/java/jdk1.7.0_79
      HADOOP_PROFILE=hadoop-2.6
      HADOOP_VERSION=
      SPARK_BRANCH=branch-2.1
      AMPLAB_JENKINS="true"
      ```

  We have been using the same convention for those variables. These are actually being used in `run-tests.py` script - here https://github.com/apache/spark/blob/master/dev/run-tests.py#L519-L520

- Revert the previous try

  After https://github.com/apache/spark/pull/17651, it seems the build still fails on SBT Hadoop 2.6 master.

  I am unable to reproduce this - https://github.com/apache/spark/pull/17477#issuecomment-294094092 and the reviewer was too. So, this got merged as it looks the only way to verify this is to merge it currently (as no one seems able to reproduce this).

## How was this patch tested?

I only checked `is_hadoop_version_2_6 = os.environ.get("AMPLAB_JENKINS_BUILD_PROFILE") == "hadoop2.6"` is working fine as expected as below:

```python
>>> import collections
>>> os = collections.namedtuple('os', 'environ')(environ={"AMPLAB_JENKINS_BUILD_PROFILE": "hadoop2.6"})
>>> print(not os.environ.get("AMPLAB_JENKINS_BUILD_PROFILE") == "hadoop2.6")
False
>>> os = collections.namedtuple('os', 'environ')(environ={"AMPLAB_JENKINS_BUILD_PROFILE": "hadoop2.7"})
>>> print(not os.environ.get("AMPLAB_JENKINS_BUILD_PROFILE") == "hadoop2.6")
True
>>> os = collections.namedtuple('os', 'environ')(environ={})
>>> print(not os.environ.get("AMPLAB_JENKINS_BUILD_PROFILE") == "hadoop2.6")
True
```

I tried many ways but I was unable to reproduce this in my local. Sean also tried the way I did but he was also unable to reproduce this.

Please refer the comments in https://github.com/apache/spark/pull/17477#issuecomment-294094092

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #17669 from HyukjinKwon/revert-SPARK-20343.

[SPARK-20343][BUILD] Force Avro 1.7.7 in sbt build to resolve build failure in SBT Hadoop 2.6 master on Jenkins

## What changes were proposed in this pull request?

This PR proposes to force Avro's version to 1.7.7 in core to resolve the build failure as below:

```
[error] /home/jenkins/workspace/spark-master-test-sbt-hadoop-2.6/core/src/main/scala/org/apache/spark/serializer/GenericAvroSerializer.scala:123: value createDatumWriter is not a member of org.apache.avro.generic.GenericData
[error]     writerCache.getOrElseUpdate(schema, GenericData.get.createDatumWriter(schema))
[error]
```

https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-master-test-sbt-hadoop-2.6/2770/consoleFull

Note that this is a hack and should be removed in the future.

## How was this patch tested?

I only tested this actually overrides the dependency.

I tried many ways but I was unable to reproduce this in my local. Sean also tried the way I did but he was also unable to reproduce this.

Please refer the comments in https://github.com/apache/spark/pull/17477#issuecomment-294094092

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #17651 from HyukjinKwon/SPARK-20343-sbt.

- Add dependency on aws-java-sdk-sts
- Replace SerializableAWSCredentials with new SerializableCredentialsProvider interface
- Make KinesisReceiver take SerializableCredentialsProvider as argument and
  pass credential provider to KCL
- Add new implementations of KinesisUtils.createStream() that take STS
  arguments
- Make JavaKinesisStreamSuite test the entire KinesisUtils Java API
- Update KCL/AWS SDK dependencies to 1.7.x/1.11.x

## What changes were proposed in this pull request?

[JIRA link with detailed description.](https://issues.apache.org/jira/browse/SPARK-19405)

* Replace SerializableAWSCredentials with new SerializableKCLAuthProvider class that takes 5 optional config params for configuring AWS auth and returns the appropriate credential provider object
* Add new public createStream() APIs for specifying these parameters in KinesisUtils

## How was this patch tested?

* Manually tested using explicit keypair and instance profile to read data from Kinesis stream in separate account (difficult to write a test orchestrating creation and assumption of IAM roles across separate accounts)
* Expanded JavaKinesisStreamSuite to test the entire Java API in KinesisUtils

## License acknowledgement
This contribution is my original work and that I license the work to the project under the project’s open source license.

Author: Budde <budde@amazon.com>

Closes #16744 from budde/master.

- Move external/java8-tests tests into core, streaming, sql and remove
- Remove MaxPermGen and related options
- Fix some reflection / TODOs around Java 8+ methods
- Update doc references to 1.7/1.8 differences
- Remove Java 7/8 related build profiles
- Update some plugins for better Java 8 compatibility
- Fix a few Java-related warnings

For the future:

- Update Java 8 examples to fully use Java 8
- Update Java tests to use lambdas for simplicity
- Update Java internal implementations to use lambdas

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #16871 from srowen/SPARK-19493.

## What changes were proposed in this pull request?

- Remove support for Hadoop 2.5 and earlier
- Remove reflection and code constructs only needed to support multiple versions at once
- Update docs to reflect newer versions
- Remove older versions' builds and profiles.

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #16810 from srowen/SPARK-19464.

## What changes were proposed in this pull request?

According to the discussion on #16281 which tried to upgrade toward Apache Parquet 1.9.0, Apache Spark community prefer to upgrade to 1.8.2 instead of 1.9.0. Now, Apache Parquet 1.8.2 is released officially last week on 26 Jan. We can use 1.8.2 now.

https://lists.apache.org/thread.html/af0c813f1419899289a336d96ec02b3bbeecaea23aa6ef69f435c142%3Cdev.parquet.apache.org%3E

This PR only aims to bump Parquet version to 1.8.2. It didn't touch any other codes.

## How was this patch tested?

Pass the existing tests and also manually by doing `./dev/test-dependencies.sh`.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #16751 from dongjoon-hyun/SPARK-19409.

**What changes were proposed in this pull request?**

Use Hadoop 2.6.5 for the Hadoop 2.6 profile, I see a bunch of fixes including security ones in the release notes that we should pick up

**How was this patch tested?**

Running the unit tests now with IBM's SDK for Java and let's see what happens with OpenJDK in the community builder - expecting no trouble as it is only a minor release.

Author: Adam Roberts <aroberts@uk.ibm.com>

Closes #16616 from a-roberts/Hadoop265Bumper.

## What changes were proposed in this pull request?

Upgrade Netty to `4.0.43.Final` to add the fix for https://github.com/netty/netty/issues/6153

## How was this patch tested?

Jenkins

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #16568 from zsxwing/SPARK-18971.

## What changes were proposed in this pull request?

Updates to libthrift 0.9.3 to address a CVE.

## How was this patch tested?

Existing tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #16530 from srowen/SPARK-18997.

Remove spark-tag's compile-scope dependency (and, indirectly, spark-core's compile-scope transitive-dependency) on scalatest by splitting test-oriented tags into spark-tags' test JAR.

Alternative to #16303.

Author: Ryan Williams <ryan.blake.williams@gmail.com>

Closes #16311 from ryan-williams/tt.

## What changes were proposed in this pull request?
I recently hit a bug of com.thoughtworks.paranamer/paranamer, which causes jackson fail to handle byte array defined in a case class. Then I find https://github.com/FasterXML/jackson-module-scala/issues/48, which suggests that it is caused by a bug in paranamer. Let's upgrade paranamer. Since we are using jackson 2.6.5 and jackson-module-paranamer 2.6.5 use com.thoughtworks.paranamer/paranamer 2.6, I suggests that we upgrade paranamer to 2.6.

Author: Yin Huai <yhuai@databricks.com>

Closes #16359 from yhuai/SPARK-18951.

## What changes were proposed in this pull request?

Upgrading KCL version from 1.6.1 to 1.6.2.  Without this upgrade, Spark cannot consume
from a stream that includes aggregated records.

This change was already commited against an older version of Spark.  We need to
apply the same thing to master.

## How was this patch tested?

Manual testing using dump.py:
https://gist.github.com/boneill42/020dde814346c6b4ad0ba28406c3ea10

Please review http://spark.apache.org/contributing.html before opening a pull request.

Author: Brian O'Neill <bone@alumni.brown.edu>

Closes #16236 from boneill42/master.

## What changes were proposed in this pull request?

* Moves yarn and mesos scheduler backends to resource-managers/ sub-directory (in preparation for https://issues.apache.org/jira/browse/SPARK-18278)
* Corresponding change in top-level pom.xml.

Ref: https://github.com/apache/spark/pull/16061#issuecomment-263649340

## How was this patch tested?

* Manual tests

/cc rxin

Author: Anirudh <ramanathana@google.com>

Closes #16092 from foxish/fix-scheduler-structure-2.

## What changes were proposed in this pull request?
This PR is to upgrade:
```
   sbt: 0.13.11 -> 0.13.13,
   zinc: 0.3.9 -> 0.3.11,
   maven-assembly-plugin: 2.6 -> 3.0.0
   maven-compiler-plugin: 3.5.1 -> 3.6.
   maven-jar-plugin: 2.6 -> 3.0.2
   maven-javadoc-plugin: 2.10.3 -> 2.10.4
   maven-source-plugin: 2.4 -> 3.0.1
   org.codehaus.mojo:build-helper-maven-plugin: 1.10 -> 1.12
   org.codehaus.mojo:exec-maven-plugin: 1.4.0 -> 1.5.0
```

The sbt release notes since the last version we used are: [v0.13.12](https://github.com/sbt/sbt/releases/tag/v0.13.12)  and [v0.13.13 ](https://github.com/sbt/sbt/releases/tag/v0.13.13).

## How was this patch tested?
Pass build and the existing tests.

Author: Weiqing Yang <yangweiqing001@gmail.com>

Closes #16069 from weiqingy/SPARK-18638.

## What changes were proposed in this pull request?

Force update to latest Netty 3.9.x, for dependencies like Flume, to resolve two CVEs. 3.9.2 is the first version that resolves both, and, this is the latest in the 3.9.x line.

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #16102 from srowen/SPARK-18586.

## What changes were proposed in this pull request?
This patch bumps master branch version to 2.2.0-SNAPSHOT.

## How was this patch tested?
N/A

Author: Reynold Xin <rxin@databricks.com>

Closes #16126 from rxin/SPARK-18695.

[SPARK-18602] Set the version of org.codehaus.janino:commons-compiler to 3.0.0 to match the version of org.codehaus.janino:janino

## What changes were proposed in this pull request?
org.codehaus.janino:janino depends on org.codehaus.janino:commons-compiler and we have been upgraded to org.codehaus.janino:janino 3.0.0.

However, seems we are still pulling in org.codehaus.janino:commons-compiler 2.7.6 because of calcite. It looks like an accident because we exclude janino from calcite (see here https://github.com/apache/spark/blob/branch-2.1/pom.xml#L1759). So, this PR upgrades org.codehaus.janino:commons-compiler to 3.0.0.

## How was this patch tested?
jenkins

Author: Yin Huai <yhuai@databricks.com>

Closes #16025 from yhuai/janino-commons-compile.

[SPARK-3359][BUILD][DOCS] More changes to resolve javadoc 8 errors that will help unidoc/genjavadoc compatibility

## What changes were proposed in this pull request?

This PR only tries to fix things that looks pretty straightforward and were fixed in other previous PRs before.

This PR roughly fixes several things as below:

- Fix unrecognisable class and method links in javadoc by changing it from `[[..]]` to `` `...` ``

  ```
  [error] .../spark/sql/core/target/java/org/apache/spark/sql/streaming/DataStreamReader.java:226: error: reference not found
  [error]    * Loads text files and returns a {link DataFrame} whose schema starts with a string column named
  ```

- Fix an exception annotation and remove code backticks in `throws` annotation

  Currently, sbt unidoc with Java 8 complains as below:

  ```
  [error] .../java/org/apache/spark/sql/streaming/StreamingQuery.java:72: error: unexpected text
  [error]    * throws StreamingQueryException, if <code>this</code> query has terminated with an exception.
  ```

  `throws` should specify the correct class name from `StreamingQueryException,` to `StreamingQueryException` without backticks. (see [JDK-8007644](https://bugs.openjdk.java.net/browse/JDK-8007644)).

- Fix `[[http..]]` to `<a href="http..."></a>`.

  ```diff
  -   * [[https://blogs.oracle.com/java-platform-group/entry/diagnosing_tls_ssl_and_https Oracle
  -   * blog page]].
  +   * <a href="https://blogs.oracle.com/java-platform-group/entry/diagnosing_tls_ssl_and_https">
  +   * Oracle blog page</a>.
  ```

   `[[http...]]` link markdown in scaladoc is unrecognisable in javadoc.

- It seems class can't have `return` annotation. So, two cases of this were removed.

  ```
  [error] .../java/org/apache/spark/mllib/regression/IsotonicRegression.java:27: error: invalid use of return
  [error]    * return New instance of IsotonicRegression.
  ```

- Fix < to `&lt;` and > to `&gt;` according to HTML rules.

- Fix `</p>` complaint

- Exclude unrecognisable in javadoc, `constructor`, `todo` and `groupname`.

## How was this patch tested?

Manually tested by `jekyll build` with Java 7 and 8

```
java version "1.7.0_80"
Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)
```

```
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)
```

Note: this does not yet make sbt unidoc suceed with Java 8 yet but it reduces the number of errors with Java 8.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #15999 from HyukjinKwon/SPARK-3359-errors.

## What changes were proposed in this pull request?

This PR proposes/fixes two things.

- Remove many errors to generate javadoc with Java8 from unrecognisable tags, `tparam` and `group`.

  ```
  [error] .../spark/mllib/target/java/org/apache/spark/ml/classification/Classifier.java:18: error: unknown tag: group
  [error]   /** group setParam */
  [error]       ^
  [error] .../spark/mllib/target/java/org/apache/spark/ml/classification/Classifier.java:8: error: unknown tag: tparam
  [error]  * tparam FeaturesType  Type of input features.  E.g., <code>Vector</code>
  [error]    ^
  ...
  ```

  It does not fully resolve the problem but remove many errors. It seems both `group` and `tparam` are unrecognisable in javadoc. It seems we can't print them pretty in javadoc in a way of `example` here because they appear differently (both examples can be found in http://spark.apache.org/docs/2.0.2/api/scala/index.html#org.apache.spark.ml.classification.Classifier).

- Print `example` in javadoc.
  Currently, there are few `example` tag in several places.

  ```
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example This operation might be used to evaluate a graph
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example We might use this operation to change the vertex values
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example This function might be used to initialize edge
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example This function might be used to initialize edge
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example This function might be used to initialize edge
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example We can use this function to compute the in-degree of each
  ./graphx/src/main/scala/org/apache/spark/graphx/Graph.scala:   * example This function is used to update the vertices with new values based on external data.
  ./graphx/src/main/scala/org/apache/spark/graphx/GraphLoader.scala:   * example Loads a file in the following format:
  ./graphx/src/main/scala/org/apache/spark/graphx/GraphOps.scala:   * example This function is used to update the vertices with new
  ./graphx/src/main/scala/org/apache/spark/graphx/GraphOps.scala:   * example This function can be used to filter the graph based on some property, without
  ./graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala: * example We can use the Pregel abstraction to implement PageRank:
  ./graphx/src/main/scala/org/apache/spark/graphx/VertexRDD.scala: * example Construct a `VertexRDD` from a plain RDD:
  ./repl/scala-2.10/src/main/scala/org/apache/spark/repl/SparkCommandLine.scala: * example new SparkCommandLine(Nil).settings
  ./repl/scala-2.10/src/main/scala/org/apache/spark/repl/SparkIMain.scala:   * example addImports("org.apache.spark.SparkContext")
  ./sql/catalyst/src/test/scala/org/apache/spark/sql/catalyst/expressions/LiteralGenerator.scala: * example {{{
  ```

**Before**

  <img width="505" alt="2016-11-20 2 43 23" src="https://cloud.githubusercontent.com/assets/6477701/20457285/26f07e1c-aecb-11e6-9ae9-d9dee66845f4.png">

**After**
  <img width="499" alt="2016-11-20 1 27 17" src="https://cloud.githubusercontent.com/assets/6477701/20457240/409124e4-aeca-11e6-9a91-0ba514148b52.png">

## How was this patch tested?

Maunally tested by `jekyll build` with Java 7 and 8

```
java version "1.7.0_80"
Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)
```

```
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)
```

Note: this does not make sbt unidoc suceed with Java 8 yet but it reduces the number of errors with Java 8.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #15939 from HyukjinKwon/SPARK-3359-javadoc.

[SPARK-18445][BUILD][DOCS] Fix the markdown for `Note:`/`NOTE:`/`Note that`/`'''Note:'''` across Scala/Java API documentation

## What changes were proposed in this pull request?

It seems in Scala/Java,

- `Note:`
- `NOTE:`
- `Note that`
- `'''Note:'''`
- `note`

This PR proposes to fix those to `note` to be consistent.

**Before**

- Scala
  ![2016-11-17 6 16 39](https://cloud.githubusercontent.com/assets/6477701/20383180/1a7aed8c-acf2-11e6-9611-5eaf6d52c2e0.png)

- Java
  ![2016-11-17 6 14 41](https://cloud.githubusercontent.com/assets/6477701/20383096/c8ffc680-acf1-11e6-914a-33460bf1401d.png)

**After**

- Scala
  ![2016-11-17 6 16 44](https://cloud.githubusercontent.com/assets/6477701/20383167/09940490-acf2-11e6-937a-0d5e1dc2cadf.png)

- Java
  ![2016-11-17 6 13 39](https://cloud.githubusercontent.com/assets/6477701/20383132/e7c2a57e-acf1-11e6-9c47-b849674d4d88.png)

## How was this patch tested?

The notes were found via

```bash
grep -r "NOTE: " . | \ # Note:|NOTE:|Note that|'''Note:'''
grep -v "// NOTE: " | \  # starting with // does not appear in API documentation.
grep -E '.scala|.java' | \ # java/scala files
grep -v Suite | \ # exclude tests
grep -v Test | \ # exclude tests
grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation
-e 'org.apache.spark.api.java.function' \ # note that this is a regular expression. So actual matches were mostly `org/apache/spark/api/java/functions ...`
-e 'org.apache.spark.api.r' \
...
```

```bash
grep -r "Note that " . | \ # Note:|NOTE:|Note that|'''Note:'''
grep -v "// Note that " | \  # starting with // does not appear in API documentation.
grep -E '.scala|.java' | \ # java/scala files
grep -v Suite | \ # exclude tests
grep -v Test | \ # exclude tests
grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation
-e 'org.apache.spark.api.java.function' \
-e 'org.apache.spark.api.r' \
...
```

```bash
grep -r "Note: " . | \ # Note:|NOTE:|Note that|'''Note:'''
grep -v "// Note: " | \  # starting with // does not appear in API documentation.
grep -E '.scala|.java' | \ # java/scala files
grep -v Suite | \ # exclude tests
grep -v Test | \ # exclude tests
grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation
-e 'org.apache.spark.api.java.function' \
-e 'org.apache.spark.api.r' \
...
```

```bash
grep -r "'''Note:'''" . | \ # Note:|NOTE:|Note that|'''Note:'''
grep -v "// '''Note:''' " | \  # starting with // does not appear in API documentation.
grep -E '.scala|.java' | \ # java/scala files
grep -v Suite | \ # exclude tests
grep -v Test | \ # exclude tests
grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation
-e 'org.apache.spark.api.java.function' \
-e 'org.apache.spark.api.r' \
...
```

And then fixed one by one comparing with API documentation/access modifiers.

After that, manually tested via `jekyll build`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #15889 from HyukjinKwon/SPARK-18437.

## What changes were proposed in this pull request?

One of the important changes for 4.0.42.Final is "Support any FileRegion implementation when using epoll transport netty/netty#5825".
In 4.0.42.Final, `MessageWithHeader` can work properly when `spark.[shuffle|rpc].io.mode` is set to epoll

## How was this patch tested?

Existing tests

Author: Guoqiang Li <witgo@qq.com>

Closes #15830 from witgo/SPARK-18375_netty-4.0.42.

## What changes were proposed in this pull request?

Try excluding org.json:json from hive-exec dep as it's Cat X now. It may be the case that it's not used by the part of Hive Spark uses anyway.

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #15798 from srowen/SPARK-18262.

[SPARK-17058][BUILD] Add maven snapshots-and-staging profile to build/test against staging artifacts

## What changes were proposed in this pull request?

Adds a `snapshots-and-staging profile` so that  RCs of projects like Hadoop and HBase can be used in developer-only build and test runs. There's a comment above the profile telling people not to use this in production.

There's no attempt to do the same for SBT, as Ivy is different.
## How was this patch tested?

Tested by building against the Hadoop 2.7.3 RC 1 JARs

without the profile (and without any local copy of the 2.7.3 artifacts), the build failed

```
mvn install -DskipTests -Pyarn,hadoop-2.7,hive -Dhadoop.version=2.7.3

...

[INFO] ------------------------------------------------------------------------
[INFO] Building Spark Project Launcher 2.1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo1.maven.org/maven2/org/apache/hadoop/hadoop-client/2.7.3/hadoop-client-2.7.3.pom
[WARNING] The POM for org.apache.hadoop:hadoop-client:jar:2.7.3 is missing, no dependency information available
Downloading: https://repo1.maven.org/maven2/org/apache/hadoop/hadoop-client/2.7.3/hadoop-client-2.7.3.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Spark Project Parent POM ........................... SUCCESS [  4.482 s]
[INFO] Spark Project Tags ................................. SUCCESS [ 17.402 s]
[INFO] Spark Project Sketch ............................... SUCCESS [ 11.252 s]
[INFO] Spark Project Networking ........................... SUCCESS [ 13.458 s]
[INFO] Spark Project Shuffle Streaming Service ............ SUCCESS [  9.043 s]
[INFO] Spark Project Unsafe ............................... SUCCESS [ 16.027 s]
[INFO] Spark Project Launcher ............................. FAILURE [  1.653 s]
[INFO] Spark Project Core ................................. SKIPPED
...
```

With the profile, the build completed

```
mvn install -DskipTests -Pyarn,hadoop-2.7,hive,snapshots-and-staging -Dhadoop.version=2.7.3
```

Author: Steve Loughran <stevel@apache.org>

Closes #14646 from steveloughran/stevel/SPARK-17058-support-asf-snapshots.

## What changes were proposed in this pull request?

`SerializationUtils.clone()` of commons-lang3 (<3.5) has a bug that breaks thread safety, which gets stack sometimes caused by race condition of initializing hash map.
See https://issues.apache.org/jira/browse/LANG-1251.

## How was this patch tested?

Existing tests.

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

Closes #15548 from ueshin/issues/SPARK-17985.

This reverts commit bfe7885a.

The commit caused build failures on Hadoop 2.2 profile:

```
[error] /scratch/rxin/spark/core/src/main/scala/org/apache/spark/util/Utils.scala:1489: value read is not a member of object org.apache.commons.io.IOUtils
[error]       var numBytes = IOUtils.read(gzInputStream, buf)
[error]                              ^
[error] /scratch/rxin/spark/core/src/main/scala/org/apache/spark/util/Utils.scala:1492: value read is not a member of object org.apache.commons.io.IOUtils
[error]         numBytes = IOUtils.read(gzInputStream, buf)
[error]                            ^
```

## What changes were proposed in this pull request?

`SerializationUtils.clone()` of commons-lang3 (<3.5) has a bug that breaks thread safety, which gets stack sometimes caused by race condition of initializing hash map.
See https://issues.apache.org/jira/browse/LANG-1251.

## How was this patch tested?

Existing tests.

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

Closes #15525 from ueshin/issues/SPARK-17985.

[SPARK-17803: Docker integration tests don't run with "Docker for Mac"](https://issues.apache.org/jira/browse/SPARK-17803)

## What changes were proposed in this pull request?

This PR upgrades the [docker-client](https://mvnrepository.com/artifact/com.spotify/docker-client) dependency from [3.6.6](https://mvnrepository.com/artifact/com.spotify/docker-client/3.6.6) to [5.0.2](https://mvnrepository.com/artifact/com.spotify/docker-client/5.0.2) to enable _Docker for Mac_ users to run the `docker-integration-tests` out of the box.

The very latest docker-client version is [6.0.0](https://mvnrepository.com/artifact/com.spotify/docker-client/6.0.0) but that has one additional dependency and no usage yet.

## How was this patch tested?

The code change was tested on Mac OS X Yosemite with both _Docker Toolbox_ as well as _Docker for Mac_ and on Linux Ubuntu 14.04.

```
$ build/mvn -Pyarn -Phadoop-2.6 -Dhadoop.version=2.6.0 -Phive -Phive-thriftserver -DskipTests clean package

$ build/mvn -Pdocker-integration-tests -Pscala-2.11 -pl :spark-docker-integration-tests_2.11 clean compile test
```

Author: Christian Kadner <ckadner@us.ibm.com>

Closes #15378 from ckadner/SPARK-17803_Docker_for_Mac.

## What changes were proposed in this pull request?

This PR adds a new project ` external/kafka-0-10-sql` for Structured Streaming Kafka source.

It's based on the design doc: https://docs.google.com/document/d/19t2rWe51x7tq2e5AOfrsM9qb8_m7BRuv9fel9i0PqR8/edit?usp=sharing

tdas did most of work and part of them was inspired by koeninger's work.

### Introduction

The Kafka source is a structured streaming data source to poll data from Kafka. The schema of reading data is as follows:

Column | Type
---- | ----
key | binary
value | binary
topic | string
partition | int
offset | long
timestamp | long
timestampType | int

The source can deal with deleting topics. However, the user should make sure there is no Spark job processing the data when deleting a topic.

### Configuration

The user can use `DataStreamReader.option` to set the following configurations.

Kafka Source's options | value | default | meaning
------ | ------- | ------ | -----
startingOffset | ["earliest", "latest"] | "latest" | The start point when a query is started, either "earliest" which is from the earliest offset, or "latest" which is just from the latest offset. Note: This only applies when a new Streaming query is started, and that resuming will always pick up from where the query left off.
failOnDataLost | [true, false] | true | Whether to fail the query when it's possible that data is lost (e.g., topics are deleted, or offsets are out of range). This may be a false alarm. You can disable it when it doesn't work as you expected.
subscribe | A comma-separated list of topics | (none) | The topic list to subscribe. Only one of "subscribe" and "subscribeParttern" options can be specified for Kafka source.
subscribePattern | Java regex string | (none) | The pattern used to subscribe the topic. Only one of "subscribe" and "subscribeParttern" options can be specified for Kafka source.
kafka.consumer.poll.timeoutMs | long | 512 | The timeout in milliseconds to poll data from Kafka in executors
fetchOffset.numRetries | int | 3 | Number of times to retry before giving up fatch Kafka latest offsets.
fetchOffset.retryIntervalMs | long | 10 | milliseconds to wait before retrying to fetch Kafka offsets

Kafka's own configurations can be set via `DataStreamReader.option` with `kafka.` prefix, e.g, `stream.option("kafka.bootstrap.servers", "host:port")`

### Usage

* Subscribe to 1 topic
```Scala
spark
  .readStream
  .format("kafka")
  .option("kafka.bootstrap.servers", "host:port")
  .option("subscribe", "topic1")
  .load()
```

* Subscribe to multiple topics
```Scala
spark
  .readStream
  .format("kafka")
  .option("kafka.bootstrap.servers", "host:port")
  .option("subscribe", "topic1,topic2")
  .load()
```

* Subscribe to a pattern
```Scala
spark
  .readStream
  .format("kafka")
  .option("kafka.bootstrap.servers", "host:port")
  .option("subscribePattern", "topic.*")
  .load()
```

## How was this patch tested?

The new unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>
Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: Shixiong Zhu <zsxwing@gmail.com>
Author: cody koeninger <cody@koeninger.org>

Closes #15102 from zsxwing/kafka-source.

This was missing, preventing code that uses javax.crypto to properly
compile in Spark.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #15204 from vanzin/SPARK-17639.

## What changes were proposed in this pull request?
Docker tests are using older version  of jersey jars (1.19),  which was used in older releases of spark.  In 2.0 releases Spark was upgraded to use 2.x verison of Jersey. After  upgrade to new versions, docker tests  are  failing with AbstractMethodError.  Now that spark is upgraded  to 2.x jersey version, using of  shaded docker jars  may not be required any more.  Removed the exclusions/overrides of jersey related classes from pom file, and changed the docker-client to use regular jar instead of shaded one.

## How was this patch tested?

Tested  using existing  docker-integration-tests

Author: sureshthalamati <suresh.thalamati@gmail.com>

Closes #15114 from sureshthalamati/docker_testfix-spark-17473.

## What changes were proposed in this pull request?
This patch bumps the Hadoop version in hadoop-2.7 profile from 2.7.2 to 2.7.3, which was recently released and contained a number of bug fixes.

## How was this patch tested?
The change should be covered by existing tests.

Author: Reynold Xin <rxin@databricks.com>

Closes #15115 from rxin/SPARK-17558.

## What changes were proposed in this pull request?
Upgrade netty-all to latest in the 4.0.x line which is 4.0.41, mentions several bug fixes and performance improvements we may find useful, see netty.io/news/2016/08/29/4-0-41-Final-4-1-5-Final.html. Initially tried to use 4.1.5 but noticed it's not backwards compatible.

## How was this patch tested?
Existing unit tests against branch-1.6 and branch-2.0 using IBM Java 8 on Intel, Power and Z architectures

Author: Adam Roberts <aroberts@uk.ibm.com>

Closes #14961 from a-roberts/netty.