## What changes were proposed in this pull request?

Only build PRs with -Pyarn if YARN code was modified.

## How was this patch tested?

Jenkins tests (will look to verify whether -Pyarn was included in the PR builder for this one.)

Author: Sean Owen <sowen@cloudera.com>

Closes #14892 from srowen/SPARK-17329.

## What changes were proposed in this pull request?

add build_profile_flags entry to mesos build module

## How was this patch tested?

unit tests

Author: Michael Gummelt <mgummelt@mesosphere.io>

Closes #14885 from mgummelt/mesos-profile.

This patch is using Apache Commons Crypto library to enable shuffle encryption support.

Author: Ferdinand Xu <cheng.a.xu@intel.com>
Author: kellyzly <kellyzly@126.com>

Closes #8880 from winningsix/SPARK-10771.

## What changes were proposed in this pull request?

Excludes the `spark-warehouse` directory from the Apache RAT checks that src/run-tests performs. `spark-warehouse` is created by some of the Spark SQL tests, as well as by `bin/spark-sql`.

## How was this patch tested?

Ran src/run-tests twice. The second time, the script failed because the first iteration
Made the change in this PR.
Ran src/run-tests a third time; RAT checks succeeded.

Author: frreiss <frreiss@us.ibm.com>

Closes #14870 from frreiss/fred-17303.

## What changes were proposed in this pull request?

Move Mesos code into a mvn module

## How was this patch tested?

unit tests
manually submitting a client mode and cluster mode job
spark/mesos integration test suite

Author: Michael Gummelt <mgummelt@mesosphere.io>

Closes #14637 from mgummelt/mesos-module.

[SPARK-16781][PYSPARK] java launched by PySpark as gateway may not be the same java used in the spark environment

## What changes were proposed in this pull request?

Update to py4j 0.10.3 to enable JAVA_HOME support

## How was this patch tested?

Pyspark tests

Author: Sean Owen <sowen@cloudera.com>

Closes #14748 from srowen/SPARK-16781.

## What changes were proposed in this pull request?

Add a configurable token manager for Spark on running on yarn.

### Current Problems ###

1. Supported token provider is hard-coded, currently only hdfs, hbase and hive are supported and it is impossible for user to add new token provider without code changes.
2. Also this problem exits in timely token renewer and updater.

### Changes In This Proposal ###

In this proposal, to address the problems mentioned above and make the current code more cleaner and easier to understand, mainly has 3 changes:

1. Abstract a `ServiceTokenProvider` as well as `ServiceTokenRenewable` interface for token provider. Each service wants to communicate with Spark through token way needs to implement this interface.
2. Provide a `ConfigurableTokenManager` to manage all the register token providers, also token renewer and updater. Also this class offers the API for other modules to obtain tokens, get renewal interval and so on.
3. Implement 3 built-in token providers `HDFSTokenProvider`, `HiveTokenProvider` and `HBaseTokenProvider` to keep the same semantics as supported today. Whether to load in these built-in token providers is controlled by configuration "spark.yarn.security.tokens.${service}.enabled", by default for all the built-in token providers are loaded.

### Behavior Changes ###

For the end user there's no behavior change, we still use the same configuration `spark.yarn.security.tokens.${service}.enabled` to decide which token provider is enabled (hbase or hive).

For user implemented token provider (assume the name of token provider is "test") needs to add into this class should have two configurations:

1. `spark.yarn.security.tokens.test.enabled` to true
2. `spark.yarn.security.tokens.test.class` to the full qualified class name.

So we still keep the same semantics as current code while add one new configuration.

### Current Status ###

- [x] token provider interface and management framework.
- [x] implement built-in token providers (hdfs, hbase, hive).
- [x] Coverage of unit test.
- [x] Integrated test with security cluster.

## How was this patch tested?

Unit test and integrated test.

Please suggest and review, any comment is greatly appreciated.

Author: jerryshao <sshao@hortonworks.com>

Closes #14065 from jerryshao/SPARK-16342.

## What changes were proposed in this pull request?
As of Scala 2.11.x there is no longer a org.scala-lang:jline version aligned to the scala version itself. Scala console now uses the plain jline:jline module. Spark's  dependency management did not reflect this change properly, causing Maven to pull in Jline via transitive dependency. Unfortunately Jline 2.12 contained a minor but very annoying bug rendering the shell almost useless for developers with german keyboard layout. This request contains the following chages:
- Exclude transitive dependency 'jline:jline' from hive-exec module
- Remove global properties 'jline.version' and 'jline.groupId'
- Add both properties and dependency to 'scala-2.11' profile
- Add explicit dependency on 'jline:jline' to  module 'spark-repl'

## How was this patch tested?
- Running mvn dependency:tree and checking for correct Jline version 2.12.1
- Running full builds with assembly and checking for jline-2.12.1.jar in 'lib' folder of generated tarball

Author: Stefan Schulze <stefan.schulze@pentasys.de>

Closes #14429 from stsc-pentasys/SPARK-16770.

## What changes were proposed in this pull request?

New config var: spark.mesos.docker.containerizer={"mesos","docker" (default)}

This adds support for running docker containers via the Mesos unified containerizer: http://mesos.apache.org/documentation/latest/container-image/

The benefit is losing the dependency on `dockerd`, and all the costs which it incurs.

I've also updated the supported Mesos version to 0.28.2 for support of the required protobufs.

This is blocked on: https://github.com/apache/spark/pull/14167

## How was this patch tested?

- manually testing jobs submitted with both "mesos" and "docker" settings for the new config var.
- spark/mesos integration test suite

Author: Michael Gummelt <mgummelt@mesosphere.io>

Closes #14275 from mgummelt/unified-containerizer.

## What changes were proposed in this pull request?

Version of derby upgraded based on important security info at VersionEye. Test scope added so we don't include it in our final package anyway. NB: I think this should be backported to all previous releases as it is a security problem https://www.versioneye.com/java/org.apache.derby:derby/10.11.1.1

The CVE number is 2015-1832. I also suggest we add a SECURITY tag for JIRAs

## How was this patch tested?
Existing tests with the change making sure that we see no new failures. I checked derby 10.12.x and not derby 10.11.x is downloaded to our ~/.m2 folder.

I then used dev/make-distribution.sh and checked the dist/jars folder for Spark 2.0: no derby jar is present.

I don't know if this would also remove it from the assembly jar in our 1.x branches.

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

Closes #14379 from a-roberts/patch-4.

## What changes were proposed in this pull request?

(Please fill in changes proposed in this fix)

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

Mesos agents by default will not pull docker images which are cached
locally already. In order to run Spark executors from mutable tags like
`:latest` this commit introduces a Spark setting
(`spark.mesos.executor.docker.forcePullImage`). Setting this flag to
true will tell the Mesos agent to force pull the docker image (default is `false` which is consistent with the previous
implementation and Mesos' default
behaviour).

Author: Philipp Hoffmann <mail@philipphoffmann.de>

Closes #14348 from philipphoffmann/force-pull-image.

This reverts commit 978cd5f1.

## What changes were proposed in this pull request?

Mesos agents by default will not pull docker images which are cached
locally already. In order to run Spark executors from mutable tags like
`:latest` this commit introduces a Spark setting
`spark.mesos.executor.docker.forcePullImage`. Setting this flag to
true will tell the Mesos agent to force pull the docker image (default is `false` which is consistent with the previous
implementation and Mesos' default
behaviour).

## How was this patch tested?

I ran a sample application including this change on a Mesos cluster and verified the correct behaviour for both, with and without, force pulling the executor image. As expected the image is being force pulled if the flag is set.

Author: Philipp Hoffmann <mail@philipphoffmann.de>

Closes #13051 from philipphoffmann/force-pull-image.

## What changes were proposed in this pull request?
This patch removes dev/audit-release. It was initially created to do basic release auditing. They have been unused by for the last one year+.

## How was this patch tested?
N/A

Author: Reynold Xin <rxin@databricks.com>

Closes #14342 from rxin/SPARK-16685.

## What changes were proposed in this pull request?
breeze 0.12 has been released for more than half a year, and it brings lots of new features, performance improvement and bug fixes.
One of the biggest features is ```LBFGS-B``` which is an implementation of ```LBFGS``` with box constraints and much faster for some special case.
We would like to implement Huber loss function for ```LinearRegression``` ([SPARK-3181](https://issues.apache.org/jira/browse/SPARK-3181)) and it requires ```LBFGS-B``` as the optimization solver. So we should bump up the dependent breeze version to 0.12.
For more features, improvements and bug fixes of breeze 0.12, you can refer the following link:
https://groups.google.com/forum/#!topic/scala-breeze/nEeRi_DcY5c

## How was this patch tested?
No new tests, should pass the existing ones.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #14150 from yanboliang/spark-16494.

## What changes were proposed in this pull request?

Add a check-cran.sh script that runs `R CMD check` as CRAN. Also fixes a number of issues pointed out by the check. These include
- Updating `DESCRIPTION` to be appropriate
- Adding a .Rbuildignore to ignore lintr, src-native, html that are non-standard files / dirs
- Adding aliases to all S4 methods in DataFrame, Column, GroupedData etc.  This is required as stated in https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-S4-classes-and-methods
- Other minor fixes

## How was this patch tested?

SparkR unit tests, running the above mentioned script

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

Closes #14173 from shivaram/sparkr-cran-changes.

## What changes were proposed in this pull request?

This PR updates version of Janino compiler from 2.7.8 to 3.0.0. This version fixes [an Janino issue](https://github.com/janino-compiler/janino/issues/1) that fixes [an issue](https://issues.apache.org/jira/browse/SPARK-15467), which throws Java exception, in Spark.

## How was this patch tested?

Manually tested using a program in [the JIRA entry](https://issues.apache.org/jira/browse/SPARK-15467)

Author: Kazuaki Ishizaki <ishizaki@jp.ibm.com>

Closes #14127 from kiszk/SPARK-15467.

## What changes were proposed in this pull request?
This PR adds hive-thriftserver profile to scala 2.10 build created by release-build.sh.

Author: Yin Huai <yhuai@databricks.com>

Closes #14108 from yhuai/SPARK-16453.

In the `dev/run-tests.py` script we check a `Popen.retcode` for success using `retcode > 0`, but this is subtlety wrong because Popen's return code will be negative if the child process was terminated by a signal: https://docs.python.org/2/library/subprocess.html#subprocess.Popen.returncode

In order to properly handle signals, we should change this to check `retcode != 0` instead.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #13692 from JoshRosen/dev-run-tests-return-code-handling.

## What changes were proposed in this pull request?

A follow up PR for #13655 to fix a wrong format tag.

## How was this patch tested?

Jenkins unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #13665 from zsxwing/fix.

## What changes were proposed in this pull request?

We should mention that users can build Spark using multiple threads to decrease build times; either here or in "Building Spark"

## How was this patch tested?

Built on machines with between one core to 192 cores using mvn -T 1C and observed faster build times with no loss in stability

In response to the question here https://issues.apache.org/jira/browse/SPARK-15821 I think we should suggest this option as we know it works for Spark and can result in faster builds

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

Closes #13562 from a-roberts/patch-3.

## What changes were proposed in this pull request?

This PR just enables tests for sql/streaming.py and also fixes the failures.

## How was this patch tested?

Existing unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #13655 from zsxwing/python-streaming-test.

## What changes were proposed in this pull request?

Updating the Hadoop version from 2.7.0 to 2.7.2 if we use the Hadoop-2.7 build profile

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Existing tests

(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

I'd like us to use Hadoop 2.7.2 owing to the Hadoop release notes stating Hadoop 2.7.0 is not ready for production use

https://hadoop.apache.org/docs/r2.7.0/ states

"Apache Hadoop 2.7.0 is a minor release in the 2.x.y release line, building upon the previous stable release 2.6.0.
This release is not yet ready for production use. Production users should use 2.7.1 release and beyond."

Hadoop 2.7.1 release notes:
"Apache Hadoop 2.7.1 is a minor release in the 2.x.y release line, building upon the previous release 2.7.0. This is the next stable release after Apache Hadoop 2.6.x."

And then Hadoop 2.7.2 release notes:
"Apache Hadoop 2.7.2 is a minor release in the 2.x.y release line, building upon the previous stable release 2.7.1."

I've tested this is OK with Intel hardware and IBM Java 8 so let's test it with OpenJDK, ideally this will be pushed to branch-2.0 and master.

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

Closes #13556 from a-roberts/patch-2.

This patch fixes a bug in `./dev/test-dependencies.sh` which caused spurious failures when the script was run on a machine with an empty `.m2` cache. The problem was that extra log output from the dependency download was conflicting with the grep / regex used to identify the classpath in the Maven output. This patch fixes this issue by adjusting the regex pattern.

Tested manually with the following reproduction of the bug:

```
rm -rf ~/.m2/repository/org/apache/commons/
./dev/test-dependencies.sh
```

Author: Josh Rosen <joshrosen@databricks.com>

Closes #13568 from JoshRosen/SPARK-12712.

## What changes were proposed in this pull request?

revived #13464

Fix Java Lint errors introduced by #13286 and #13280
Before:
```
Using `mvn` from path: /Users/pichu/Project/spark/build/apache-maven-3.3.9/bin/mvn
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=512M; support was removed in 8.0
Checkstyle checks failed at following occurrences:
[ERROR] src/main/java/org/apache/spark/launcher/LauncherServer.java:[340,5] (whitespace) FileTabCharacter: Line contains a tab character.
[ERROR] src/main/java/org/apache/spark/launcher/LauncherServer.java:[341,5] (whitespace) FileTabCharacter: Line contains a tab character.
[ERROR] src/main/java/org/apache/spark/launcher/LauncherServer.java:[342,5] (whitespace) FileTabCharacter: Line contains a tab character.
[ERROR] src/main/java/org/apache/spark/launcher/LauncherServer.java:[343,5] (whitespace) FileTabCharacter: Line contains a tab character.
[ERROR] src/main/java/org/apache/spark/sql/streaming/OutputMode.java:[41,28] (naming) MethodName: Method name 'Append' must match pattern '^[a-z][a-z0-9][a-zA-Z0-9_]*$'.
[ERROR] src/main/java/org/apache/spark/sql/streaming/OutputMode.java:[52,28] (naming) MethodName: Method name 'Complete' must match pattern '^[a-z][a-z0-9][a-zA-Z0-9_]*$'.
[ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/SpecificParquetRecordReaderBase.java:[61,8] (imports) UnusedImports: Unused import - org.apache.parquet.schema.PrimitiveType.
[ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/SpecificParquetRecordReaderBase.java:[62,8] (imports) UnusedImports: Unused import - org.apache.parquet.schema.Type.
```

## How was this patch tested?
ran `dev/lint-java` locally

Author: Sandeep Singh <sandeep@techaddict.me>

Closes #13559 from techaddict/minor-3.

## What changes were proposed in this pull request?

This reverts commit c24b6b67. Sent a PR to run Jenkins tests due to the revert conflicts of `dev/deps/spark-deps-hadoop*`.

## How was this patch tested?

Jenkins unit tests, integration tests, manual tests)

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #13417 from zsxwing/revert-SPARK-11753.

## What changes were proposed in this pull request?

This includes minimal changes to get Spark using the current release of Parquet, 1.8.1.

## How was this patch tested?

This uses the existing Parquet tests.

Author: Ryan Blue <blue@apache.org>

Closes #13280 from rdblue/SPARK-9876-update-parquet.

## What changes were proposed in this pull request?

See https://issues.apache.org/jira/browse/SPARK-15523

This PR replaces PR #13293. It's isolated to a new branch, and contains some more squashed changes.

## How was this patch tested?

1. Executed `mvn clean package` in `mllib` directory
2. Executed `dev/test-dependencies.sh --replace-manifest` in the root directory.

Author: Villu Ruusmann <villu.ruusmann@gmail.com>

Closes #13297 from vruusmann/update-jpmml.

## What changes were proposed in this pull request?
The ANTLR4 SBT plugin has been moved from its own repo to one on bintray. The version was also changed from `0.7.10` to `0.7.11`. The latter actually broke our build (ihji has fixed this by also adding `0.7.10` and others to the bin-tray repo).

This PR upgrades the SBT-ANTLR4 plugin and ANTLR4 to their most recent versions (`0.7.11`/`4.5.3`). I have also removed a few obsolete build configurations.

## How was this patch tested?
Manually running SBT/Maven builds.

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #13299 from hvanhovell/SPARK-15525.

## What changes were proposed in this pull request?

Default QuoteEscapingEnabled flag to true when writing CSV and add an escapeQuotes option to be able to change this.

See https://github.com/uniVocity/univocity-parsers/blob/f3eb2af26374940e60d91d1703bde54619f50c51/src/main/java/com/univocity/parsers/csv/CsvWriterSettings.java#L231-L247

This change is needed to be able to write RFC 4180 compatible CSV files (https://tools.ietf.org/html/rfc4180#section-2)

https://issues.apache.org/jira/browse/SPARK-15493

## How was this patch tested?

Added a test that verifies the output is quoted correctly.

Author: Jurriaan Pruis <email@jurriaanpruis.nl>

Closes #13267 from jurriaan/quote-escaping.

## What changes were proposed in this pull request?

Jackson suppprts `allowNonNumericNumbers` option to parse non-standard non-numeric numbers such as "NaN", "Infinity", "INF".  Currently used Jackson version (2.5.3) doesn't support it all. This patch upgrades the library and make the two ignored tests in `JsonParsingOptionsSuite` passed.

## How was this patch tested?

`JsonParsingOptionsSuite`.

Author: Liang-Chi Hsieh <simonh@tw.ibm.com>
Author: Liang-Chi Hsieh <viirya@appier.com>

Closes #9759 from viirya/fix-json-nonnumric.

## What changes were proposed in this pull request?
I initially asked to create a hivecontext-compatibility module to put the HiveContext there. But we are so close to Spark 2.0 release and there is only a single class in it. It seems overkill to have an entire package, which makes it more inconvenient, for a single class.

## How was this patch tested?
Tests were moved.

Author: Reynold Xin <rxin@databricks.com>

Closes #13207 from rxin/SPARK-15424.

## What changes were proposed in this pull request?

Now that SparkSQL supports all TPC-DS queries, this patch adds all 99 benchmark queries inside SparkSQL.

## How was this patch tested?

Benchmark only

Author: Sameer Agarwal <sameer@databricks.com>

Closes #13188 from sameeragarwal/tpcds-all.

## What changes were proposed in this pull request?

Once SPARK-14487 and SPARK-14549 are merged, we will migrate to use the new vector and matrix type in the new ml pipeline based apis.

## How was this patch tested?

Unit tests

Author: DB Tsai <dbt@netflix.com>
Author: Liang-Chi Hsieh <simonh@tw.ibm.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #12627 from dbtsai/SPARK-14615-NewML.

## What changes were proposed in this pull request?

(See https://github.com/apache/spark/pull/12416 where most of this was already reviewed and committed; this is just the module structure and move part. This change does not move the annotations into test scope, which was the apparently problem last time.)

Rename `spark-test-tags` -> `spark-tags`; move common annotations like `Since` to `spark-tags`

## How was this patch tested?

Jenkins tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #13074 from srowen/SPARK-15290.

[SPARK-12972][CORE][TEST-MAVEN][TEST-HADOOP2.2] Update org.apache.httpcomponents.httpclient, commons-io

## What changes were proposed in this pull request?

This is sort of a hot-fix for https://github.com/apache/spark/pull/13117, but, the problem is limited to Hadoop 2.2. The change is to manage `commons-io` to 2.4 for all Hadoop builds, which is only a net change for Hadoop 2.2, which was using 2.1.

## How was this patch tested?

Jenkins tests -- normal PR builder, then the `[test-hadoop2.2] [test-maven]` if successful.

Author: Sean Owen <sowen@cloudera.com>

Closes #13132 from srowen/SPARK-12972.3.

## What changes were proposed in this pull request?

(Retry of https://github.com/apache/spark/pull/13049)

- update to httpclient 4.5 / httpcore 4.4
- remove some defunct exclusions
- manage httpmime version to match
- update selenium / httpunit to support 4.5 (possible now that Jetty 9 is used)

## How was this patch tested?

Jenkins tests. Also, locally running the same test command of one Jenkins profile that failed: `mvn -Phadoop-2.6 -Pyarn -Phive -Phive-thriftserver -Pkinesis-asl ...`

Author: Sean Owen <sowen@cloudera.com>

Closes #13117 from srowen/SPARK-12972.2.

This reverts commit c74a6c3f.

## What changes were proposed in this pull request?

- update httpcore/httpclient to latest
- centralize version management
- remove excludes that are no longer relevant according to SBT/Maven dep graphs
- also manage httpmime to match httpclient

## How was this patch tested?

Jenkins tests, plus review of dependency graphs from SBT/Maven, and review of test-dependencies.sh  output

Author: Sean Owen <sowen@cloudera.com>

Closes #13049 from srowen/SPARK-12972.

## What changes were proposed in this pull request?

This upgrades to Py4J 0.10.1 which reduces syscal overhead in Java gateway ( see https://github.com/bartdag/py4j/issues/201 ). Related https://issues.apache.org/jira/browse/SPARK-6728 .

## How was this patch tested?

Existing doctests & unit tests pass

Author: Holden Karau <holden@us.ibm.com>

Closes #13064 from holdenk/SPARK-15061-upgrade-to-py4j-0.10.1.