This reverts commit f6ff2a61.

(This is a replacement of #1399, trying to fix potential `HiveThriftServer2` port collision between parallel builds. Please refer to [these comments](https://github.com/apache/spark/pull/1399#issuecomment-50212572) for details.)

JIRA issue: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)

Merging the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1600 from liancheng/jdbc and squashes the following commits:

ac4618b [Cheng Lian] Uses random port for HiveThriftServer2 to avoid collision with parallel builds
090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server

This reverts commit 06dc0d2c.

#1399 is making Jenkins fail.  We should investigate and put this back after its passing tests.

Author: Michael Armbrust <michael@databricks.com>

Closes #1594 from marmbrus/revertJDBC and squashes the following commits:

59748da [Michael Armbrust] Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"

Add genjavadocSettings back to SparkBuild. It requires #1585 .

https://issues.apache.org/jira/browse/SPARK-2682

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

Closes #1584 from yhuai/SPARK-2682 and squashes the following commits:

2e89461 [Yin Huai] Merge remote-tracking branch 'upstream/master' into SPARK-2682
54e3b66 [Yin Huai] Add genjavadocSettings back.

JIRA issue:

- Main: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)
- Related: [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678)

Cherry picked the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

(Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.)

TODO

- [x] Use `spark-submit` to launch the server, the CLI and beeline
- [x] Migration guideline draft for Shark users

----

Hit by a bug in `SparkSubmitArguments` while working on this PR: all application options that are recognized by `SparkSubmitArguments` are stolen as `SparkSubmit` options. For example:

```bash
$ spark-submit --class org.apache.hive.beeline.BeeLine spark-internal --help
```

This actually shows usage information of `SparkSubmit` rather than `BeeLine`.

~~Fixed this bug here since the `spark-internal` related stuff also touches `SparkSubmitArguments` and I'd like to avoid conflict.~~

**UPDATE** The bug mentioned above is now tracked by [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678). Decided to revert changes to this bug since it involves more subtle considerations and worth a separate PR.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1399 from liancheng/thriftserver and squashes the following commits:

090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server

[SPARK-2474][SQL] For a registered table in OverrideCatalog, the Analyzer failed to resolve references in the format of "tableName.fieldName"

Please refer to JIRA (https://issues.apache.org/jira/browse/SPARK-2474) for how to reproduce the problem and my understanding of the root cause.

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

Closes #1406 from yhuai/SPARK-2474 and squashes the following commits:

96b1627 [Yin Huai] Merge remote-tracking branch 'upstream/master' into SPARK-2474
af36d65 [Yin Huai] Fix comment.
be86ba9 [Yin Huai] Correct SQL console settings.
c43ad00 [Yin Huai] Wrap the relation in a Subquery named by the table name in OverrideCatalog.lookupRelation.
a5c2145 [Yin Huai] Support sql/console.

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

Closes #1398 from ueshin/issues/SPARK-2467 and squashes the following commits:

7f01d58 [Takuya UESHIN] Revert SparkBuild to publish-local to both .m2 and .ivy2.

NOTE: It is not possible to use both env variable  `SBT_MAVEN_PROFILES`  and `-P` flag at same time. `-P` if specified takes precedence.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #1374 from ScrapCodes/SPARK-2437/rename-MAVEN_PROFILES and squashes the following commits:

8694bde [Prashant Sharma] [SPARK-2437] Rename MAVEN_PROFILES to SBT_MAVEN_PROFILES and add SBT_MAVEN_PROPERTIES

Patch introduces the new way of working also retaining the existing ways of doing things.

For example build instruction for yarn in maven is
`mvn -Pyarn -PHadoop2.2 clean package -DskipTests`
in sbt it can become
`MAVEN_PROFILES="yarn, hadoop-2.2" sbt/sbt clean assembly`
Also supports
`sbt/sbt -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0 clean assembly`

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #772 from ScrapCodes/sbt-maven and squashes the following commits:

a8ac951 [Prashant Sharma] Updated sbt version.
62b09bb [Prashant Sharma] Improvements.
fa6221d [Prashant Sharma] Excluding sql from mima
4b8875e [Prashant Sharma] Sbt assembly no longer builds tools by default.
72651ca [Prashant Sharma] Addresses code reivew comments.
acab73d [Prashant Sharma] Revert "Small fix to run-examples script."
ac4312c [Prashant Sharma] Revert "minor fix"
6af91ac [Prashant Sharma] Ported oldDeps back. + fixes issues with prev commit.
65cf06c [Prashant Sharma] Servelet API jars mess up with the other servlet jars on the class path.
446768e [Prashant Sharma] minor fix
89b9777 [Prashant Sharma] Merge conflicts
d0a02f2 [Prashant Sharma] Bumped up pom versions, Since the build now depends on pom it is better updated there. + general cleanups.
dccc8ac [Prashant Sharma] updated mima to check against 1.0
a49c61b [Prashant Sharma] Fix for tools jar
a2f5ae1 [Prashant Sharma] Fixes a bug in dependencies.
cf88758 [Prashant Sharma] cleanup
9439ea3 [Prashant Sharma] Small fix to run-examples script.
96cea1f [Prashant Sharma] SPARK-1776 Have Spark's SBT build read dependencies from Maven.
36efa62 [Patrick Wendell] Set project name in pom files and added eclipse/intellij plugins.
4973dbd [Patrick Wendell] Example build using pom reader.

Fix for class of test suite failures in jenkins

Author: Peter MacKinnon <pmackinn@redhat.com>

Closes #1271 from pdmack/master and squashes the following commits:

cfe59fd [Peter MacKinnon] exclude servlet-api in hadoop-client for sbt
6f39fec [Peter MacKinnon] add exclusion for old servlet-api on hadoop-client in core

- JavaAPISuite was trying to compare a bare path with a URI. Fix by
  extracting the path from the URI, since we know it should be a
  local path anyway/

- b9be1609 excluded the ASM dependency everywhere, but easymock needs
  it (because cglib needs it). So re-add the dependency, with test
  scope this time.

The second one above actually uncovered a weird situation: the maven
test target works, even though I can't find the class sbt complains
about in its classpath. sbt complains with:

  [error] Uncaught exception when running org.apache.spark.util
  .random.RandomSamplerSuite: java.lang.NoClassDefFoundError:
  org/objectweb/asm/Type

To avoid more weirdness caused by that, I explicitly added the asm
dependency to both maven and sbt (for tests only), and verified
the classes don't end up in the final assembly.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #917 from vanzin/flaky-tests and squashes the following commits:

d022320 [Marcelo Vanzin] Fix some tests.

JIRA: https://issues.apache.org/jira/browse/SPARK-2060

Programming guide: http://yhuai.github.io/site/sql-programming-guide.html

Scala doc of SQLContext: http://yhuai.github.io/site/api/scala/index.html#org.apache.spark.sql.SQLContext

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

Closes #999 from yhuai/newJson and squashes the following commits:

227e89e [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
ce8eedd [Yin Huai] rxin's comments.
bc9ac51 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
94ffdaa [Yin Huai] Remove "get" from method names.
ce31c81 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
e2773a6 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
79ea9ba [Yin Huai] Fix typos.
5428451 [Yin Huai] Newline
1f908ce [Yin Huai] Remove extra line.
d7a005c [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
7ea750e [Yin Huai] marmbrus's comments.
6a5f5ef [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
83013fb [Yin Huai] Update Java Example.
e7a6c19 [Yin Huai] SchemaRDD.javaToPython should convert a field with the StructType to a Map.
6d20b85 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
4fbddf0 [Yin Huai] Programming guide.
9df8c5a [Yin Huai] Python API.
7027634 [Yin Huai] Java API.
cff84cc [Yin Huai] Use a SchemaRDD for a JSON dataset.
d0bd412 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
ab810b0 [Yin Huai] Make JsonRDD private.
6df0891 [Yin Huai] Apache header.
8347f2e [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
66f9e76 [Yin Huai] Update docs and use the entire dataset to infer the schema.
8ffed79 [Yin Huai] Update the example.
a5a4b52 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
4325475 [Yin Huai] If a sampled dataset is used for schema inferring, update the schema of the JsonTable after first execution.
65b87f0 [Yin Huai] Fix sampling...
8846af5 [Yin Huai] API doc.
52a2275 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
0387523 [Yin Huai] Address PR comments.
666b957 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
a2313a6 [Yin Huai] Address PR comments.
f3ce176 [Yin Huai] After type conflict resolution, if a NullType is found, StringType is used.
0576406 [Yin Huai] Add Apache license header.
af91b23 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
f45583b [Yin Huai] Infer the schema of a JSON dataset (a text file with one JSON object per line or a RDD[String] with one JSON object per string) and returns a SchemaRDD.
f31065f [Yin Huai] A query plan or a SchemaRDD can print out its schema.

Modified the takeSample method in RDD to use the ScaSRS sampling technique to improve performance. Added a private method that computes sampling rate > sample_size/total to ensure sufficient sample size with success rate >= 0.9999. Added a unit test for the private method to validate choice of sampling rate.

Author: Doris Xin <doris.s.xin@gmail.com>
Author: dorx <doris.s.xin@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #916 from dorx/takeSample and squashes the following commits:

5b061ae [Doris Xin] merge master
444e750 [Doris Xin] edge cases
3de882b [dorx] Merge pull request #2 from mengxr/SPARK-1939
82dde31 [Xiangrui Meng] update pyspark's takeSample
48d954d [Doris Xin] remove unused imports from RDDSuite
fb1452f [Doris Xin] allowing num to be greater than count in all cases
1481b01 [Doris Xin] washing test tubes and making coffee
dc699f3 [Doris Xin] give back imports removed by accident in rdd.py
64e445b [Doris Xin] logwarnning as soon as it enters the while loop
55518ed [Doris Xin] added TODO for logging in rdd.py
eff89e2 [Doris Xin] addressed reviewer comments.
ecab508 [Doris Xin] "fixed checkstyle violation
0a9b3e3 [Doris Xin] "reviewer comment addressed"
f80f270 [Doris Xin] Merge branch 'master' into takeSample
ae3ad04 [Doris Xin] fixed edge cases to prevent overflow
065ebcd [Doris Xin] Merge branch 'master' into takeSample
9bdd36e [Doris Xin] Check sample size and move computeFraction
e3fd6a6 [Doris Xin] Merge branch 'master' into takeSample
7cab53a [Doris Xin] fixed import bug in rdd.py
ffea61a [Doris Xin] SPARK-1939: Refactor takeSample method in RDD
1441977 [Doris Xin] SPARK-1939 Refactor takeSample method in RDD to use ScaSRS

(This change is actually small, I moved some logic into
compute-classpath that was previously in spark-class).

Assemble deps has existed for a while to allow developers to
run local code with new changes quickly. When I'm developing I
typically use a simpler approach which just prepends the Spark
classes to the classpath before the assembly jar. This is well
defined in the JVM and the Spark classes take precedence over those
in the assembly.

This approach is portable across both builds which is the main reason I'd
like to switch to it. It's also a bit easier to toggle on and off quickly.

The way you use this is the following:
```
$ ./bin/spark-shell # Use spark with the normal assembly
$ export SPARK_PREPEND_CLASSES=true
$ ./bin/spark-shell # Now it's using compiled classes
$ unset SPARK_PREPEND_CLASSES
$ ./bin/spark-shell # Back to normal
```

Author: Patrick Wendell <pwendell@gmail.com>

Closes #877 from pwendell/assemble-deps and squashes the following commits:

8a11345 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into assemble-deps
faa3168 [Patrick Wendell] Adding a warning for compatibility
3f151a7 [Patrick Wendell] Small fix
bbfb73c [Patrick Wendell] Review feedback
328e9f8 [Patrick Wendell] SPARK-1843: Replace assemble-deps with env variable.

Fixes SPARK 2070 and 2071

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #1021 from ScrapCodes/SPARK-2070/package-private-methods and squashes the following commits:

7979a57 [Prashant Sharma] addressed code review comments
558546d [Prashant Sharma] A little fancy error message.
59275ab [Prashant Sharma] SPARK-2071 Mima ignores classes and its members from previous versions too.
0c4ff2b [Prashant Sharma] SPARK-2070 Ignore methods along with annotated classes.

Author: witgo <witgo@qq.com>

Closes #713 from witgo/scalatest and squashes the following commits:

b627a6a [witgo] merge master
51fb3d6 [witgo] merge master
3771474 [witgo] fix RDDSuite
996d6f9 [witgo] fix TimeStampedWeakValueHashMap test
9dfa4e7 [witgo] merge bug
1479b22 [witgo] merge master
29b9194 [witgo] fix code style
022a7a2 [witgo] fix test dependency
a52c0fa [witgo] fix test dependency
cd8f59d [witgo] Merge branch 'master' of https://github.com/apache/spark into scalatest
046540d [witgo] fix RDDSuite.scala
2c543b9 [witgo] fix ReplSuite.scala
c458928 [witgo] update scalatest to version 2.1.5

This avoids having junit classes showing up in the assembly jar.
I verified that only test classes in the jtransforms package
use junit.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #794 from vanzin/junit-dep-exclusion and squashes the following commits:

274e1c2 [Marcelo Vanzin] Remove junit from assembly in sbt build also.
ad950be [Marcelo Vanzin] Remove compile-scoped junit dependency.

I also corrected some errors made in the previous HLL count approximate API, including relativeSD wasn't really a measure for error (and we used it to test error bounds in test results).

Author: Reynold Xin <rxin@apache.org>

Closes #897 from rxin/hll and squashes the following commits:

4d83f41 [Reynold Xin] New error bound and non-randomness.
f154ea0 [Reynold Xin] Added a comment on the value bound for testing.
e367527 [Reynold Xin] One more round of code review.
41e649a [Reynold Xin] Update final mima list.
9e320c8 [Reynold Xin] Incorporate code review feedback.
e110d70 [Reynold Xin] Merge branch 'master' into hll
354deb8 [Reynold Xin] Added comment on the Mima exclude rules.
acaa524 [Reynold Xin] Added the right exclude rules in MimaExcludes.
6555bfe [Reynold Xin] Added a default method and re-arranged MimaExcludes.
1db1522 [Reynold Xin] Excluded util.SerializableHyperLogLog from MIMA check.
9221b27 [Reynold Xin] Merge branch 'master' into hll
88cfe77 [Reynold Xin] Updated documentation and restored the old incorrect API to maintain API compatibility.
1294be6 [Reynold Xin] Updated HLL+.
e7786cb [Reynold Xin] Merge branch 'master' into hll
c0ef0c2 [Reynold Xin] SPARK-1941: Update streamlib to 2.7.0 and use HyperLogLogPlus instead of HyperLogLog.

Allow Spark to build against particular Pivotal HD distributions. For example to build Spark against Pivotal HD 2.0.1 one can run:
```
mvn -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0-gphd-3.0.1.0 -DskipTests clean package
```

Author: tzolov <christian.tzolov@gmail.com>

Closes #942 from tzolov/master and squashes the following commits:

bc3e05a [tzolov] Add support for Pivotal HD in the Maven build and SBT build: [SPARK-1992]

Due to the way spark-shell launches from an assembly jar, I don't think this change will affect anyone who isn't trying to launch the shell directly from sbt.  That said, it is kinda nice to be able to launch all things directly from SBT when developing.

Author: Michael Armbrust <michael@databricks.com>

Closes #801 from marmbrus/hiveRepl and squashes the following commits:

9570571 [Michael Armbrust] Optionally include Hive as a dependency of the REPL.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #910 from ScrapCodes/enable-mima/spark-core and squashes the following commits:

79f3687 [Prashant Sharma] updated Mima to check against version 1.0
1e8969c [Prashant Sharma] Spark core missed out on Mima settings. So in effect we never tested spark core for mima related errors.

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

Closes #889 from yhuai/SPARK-1935 and squashes the following commits:

7d50ef1 [Yin Huai] Explicitly add commons-codec 1.5 as a dependency.

Author: witgo <witgo@qq.com>

Closes #824 from witgo/SPARK-1875_commons-lang-2.6 and squashes the following commits:

ef7231d [witgo] review commit
ead3c3b [witgo] SPARK-1875:NoClassDefFoundError: StringUtils when building against Hadoop 1

Author: witgo <witgo@qq.com>

Closes #754 from witgo/commons-lang and squashes the following commits:

3ebab31 [witgo] merge master
f3b8fa2 [witgo] merge master
2083fae [witgo] repeat definition
5599cdb [witgo] multiple version of sbt  dependency
c1b66a1 [witgo] fix different versions of commons-lang dependency

Author: witgo <witgo@qq.com>

Closes #773 from witgo/sbt_javaOptions and squashes the following commits:

26c7d38 [witgo] Improve sbt configuration

See https://issues.apache.org/jira/browse/SPARK-1828 for more information.

This is being submitted to Jenkin's for testing. The dependency won't fully
propagate in Maven central for a few more hours.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #767 from pwendell/hive-shaded and squashes the following commits:

ea10ac5 [Patrick Wendell] SPARK-1828: Created forked version of hive-exec that doesn't bundle other dependencies

Enabled Mesos (0.18.1) dependency with shaded protobuf

Why is this needed?
Avoids any protobuf version collision between Mesos and any other
dependency in Spark e.g. Hadoop HDFS 2.2+ or 1.0.4.

Ticket: https://issues.apache.org/jira/browse/SPARK-1806

* Should close https://issues.apache.org/jira/browse/SPARK-1433

Author berngp

Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>

Closes #741 from berngp/feature/SPARK-1806 and squashes the following commits:

5d70646 [Bernardo Gomez Palacio] SPARK-1806: Upgrade Mesos dependency to 0.18.1

More info at. https://github.com/sbt/sbt/issues/1010

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #525 from ScrapCodes/sbt-inc-opt and squashes the following commits:

ba8fa42 [Prashant Sharma] Enabled incremental build that comes with sbt 0.13.2

TL;DR is there is a bit of JAR hell trouble with Netty, that can be mostly resolved and will resolve a test failure.

I hit the error described at http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-startup-time-out-td1753.html while running FlumeStreamingSuite, and have for a short while (is it just me?)

velvia notes:
"I have found a workaround.  If you add akka 2.2.4 to your dependencies, then everything works, probably because akka 2.2.4 brings in newer version of Jetty."

There are at least 3 versions of Netty in play in the build:

- the new Flume 1.4.0 dependency brings in io.netty:netty:3.4.0.Final, and that is the immediate problem
- the custom version of akka 2.2.3 depends on io.netty:netty:3.6.6.
- but, Spark Core directly uses io.netty:netty-all:4.0.17.Final

The POMs try to exclude other versions of netty, but are excluding org.jboss.netty:netty, when in fact older versions of io.netty:netty (not netty-all) are also an issue.

The org.jboss.netty:netty excludes are largely unnecessary. I replaced many of them with io.netty:netty exclusions until everything agreed on io.netty:netty-all:4.0.17.Final.

But this didn't work, since Akka 2.2.3 doesn't work with Netty 4.x. Down-grading to 3.6.6.Final across the board made some Spark code not compile.

If the build *keeps* io.netty:netty:3.6.6.Final as well, everything seems to work. Part of the reason seems to be that Netty 3.x used the old `org.jboss.netty` packages. This is less than ideal, but is no worse than the current situation.

So this PR resolves the issue and improves the JAR hell, even if it leaves the existing theoretical Netty 3-vs-4 conflict:

- Remove org.jboss.netty excludes where possible, for clarity; they're not needed except with Hadoop artifacts
- Add io.netty:netty excludes where needed -- except, let akka keep its io.netty:netty
- Change a bit of test code that actually depended on Netty 3.x, to use 4.x equivalent
- Update SBT build accordingly

A better change would be to update Akka far enough such that it agrees on Netty 4.x, but I don't know if that's feasible.

Author: Sean Owen <sowen@cloudera.com>

Closes #723 from srowen/SPARK-1789 and squashes the following commits:

43661b7 [Sean Owen] Update and add Netty excludes to prevent some JAR conflicts that cause test issues

I think we are hitting this issue in some perf tests: https://github.com/Parquet/parquet-mr/commit/6aed5288fd4a1398063a5a219b2ae4a9f71b02cf

Credit to @aarondav !

Author: Michael Armbrust <michael@databricks.com>

Closes #684 from marmbrus/upgradeParquet and squashes the following commits:

e10a619 [Michael Armbrust] Upgrade parquet library.

Author: witgo <witgo@qq.com>

Closes #688 from witgo/SPARK-1644 and squashes the following commits:

56ad6ac [witgo] review commit
87c03e4 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1644
6ffa7e4 [witgo] review commit
a597414 [witgo] The org.datanucleus:* should not be packaged into spark-assembly-*.jar

This PR updates spark-submit to allow submitting Python scripts (currently only with deploy-mode=client, but that's all that was supported before) and updates the PySpark code to properly find various paths, etc. One significant change is that we assume we can always find the Python files either from the Spark assembly JAR (which will happen with the Maven assembly build in make-distribution.sh) or from SPARK_HOME (which will exist in local mode even if you use sbt assembly, and should be enough for testing). This means we no longer need a weird hack to modify the environment for YARN.

This patch also updates the Python worker manager to run python with -u, which means unbuffered output (send it to our logs right away instead of waiting a while after stuff was written); this should simplify debugging.

In addition, it fixes https://issues.apache.org/jira/browse/SPARK-1709, setting the main class from a JAR's Main-Class attribute if not specified by the user, and fixes a few help strings and style issues in spark-submit.

In the future we may want to make the `pyspark` shell use spark-submit as well, but it seems unnecessary for 1.0.

Author: Matei Zaharia <matei@databricks.com>

Closes #664 from mateiz/py-submit and squashes the following commits:

15e9669 [Matei Zaharia] Fix some uses of path.separator property
051278c [Matei Zaharia] Small style fixes
0afe886 [Matei Zaharia] Add license headers
4650412 [Matei Zaharia] Add pyFiles to PYTHONPATH in executors, remove old YARN stuff, add tests
15f8e1e [Matei Zaharia] Set PYTHONPATH in PythonWorkerFactory in case it wasn't set from outside
47c0655 [Matei Zaharia] More work to make spark-submit work with Python:
d4375bd [Matei Zaharia] Clean up description of spark-submit args a bit and add Python ones

We use org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter in spark on yarn but are not included it in the assembly jar.

I tested this on yarn cluster by removing the yarn jars from the classpath and spark runs fine now.

Author: Thomas Graves <tgraves@apache.org>

Closes #406 from tgravescs/SPARK-1474 and squashes the following commits:

1548bf9 [Thomas Graves] SPARK-1474: Spark on yarn assembly doesn't include org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter

See related discussion at https://github.com/apache/spark/pull/468

This PR may still overstep what you have in mind, but let me put it on the table to start. Besides fixing the issue, it has one substantive change, and that is to manage Hadoop-specific things only in Hadoop-related profiles. This does _not_ remove `yarn.version`.

- Moves the YARN and Hadoop profiles together in pom.xml. Sorry that this makes the diff a little hard to grok but the changes are only as follows.
- Removes `hadoop.major.version`
- Introduce `hadoop-2.2` and `hadoop-2.3` profiles to control Hadoop-specific changes:
  - like the protobuf version issue - this was only 'solved' now by enabling YARN for 2.2+, which is really an orthogonal issue
  - like the jets3t version issue now
- Hadoop profiles set an appropriate default `hadoop.version`, that can be overridden
- _(YARN profiles in the parent now only exist to add the sub-module)_
- Fixes the jets3t dependency issue
 - and makes it a runtime dependency
 - and centralizes config of this guy in the parent pom
- Updates build docs
- Updates SBT build too
  - and fixes a regex problem along the way

Author: Sean Owen <sowen@cloudera.com>

Closes #629 from srowen/SPARK-1556 and squashes the following commits:

c3fa967 [Sean Owen] Fix hadoop-2.4 profile typo in doc
a2105fd [Sean Owen] Add hadoop-2.4 profile and don't set hadoop.version in profiles
274f4f9 [Sean Owen] Make jets3t a runtime dependency, and bring its exclusion up into parent config
bbed826 [Sean Owen] Use jets3t 0.9.0 for Hadoop 2.3+ (and correct similar regex issue in SBT build)
f21f356 [Sean Owen] Build changes to set up for jets3t fix

SPARK-1629. Addendum: Depend on commons lang3 (already used by tachyon) as it's used in ReplSuite, and return to use lang3 utility in Utils.scala

For consideration. This was proposed in related discussion: https://github.com/apache/spark/pull/569

Author: Sean Owen <sowen@cloudera.com>

Closes #635 from srowen/SPARK-1629.2 and squashes the following commits:

a442b98 [Sean Owen] Depend on commons lang3 (already used by tachyon) as it's used in ReplSuite, and return to use lang3 utility in Utils.scala

* `NaiveBayes` -> `SparseNaiveBayes`
* `KMeans` -> `DenseKMeans`
* `SVMWithSGD` and `LogisticRegerssionWithSGD` -> `BinaryClassification`
* `ALS` -> `MovieLensALS`
* `LinearRegressionWithSGD`, `LassoWithSGD`, and `RidgeRegressionWithSGD` -> `LinearRegression`
* `DecisionTree` -> `DecisionTreeRunner`

`scopt` is used for parsing command-line parameters. `scopt` has MIT license and it only depends on `scala-library`.

Example help message:

~~~
BinaryClassification: an example app for binary classification.
Usage: BinaryClassification [options] <input>

  --numIterations <value>
        number of iterations
  --stepSize <value>
        initial step size, default: 1.0
  --algorithm <value>
        algorithm (SVM,LR), default: LR
  --regType <value>
        regularization type (L1,L2), default: L2
  --regParam <value>
        regularization parameter, default: 0.1
  <input>
        input paths to labeled examples in LIBSVM format
~~~

Author: Xiangrui Meng <meng@databricks.com>

Closes #584 from mengxr/mllib-main and squashes the following commits:

7b58c60 [Xiangrui Meng] minor
6e35d7e [Xiangrui Meng] make imports explicit and fix code style
c6178c9 [Xiangrui Meng] update TS PCA/SVD to use new spark-submit
6acff75 [Xiangrui Meng] use scopt for DecisionTreeRunner
be86069 [Xiangrui Meng] use main instead of extending App
b3edf68 [Xiangrui Meng] move DecisionTree's main method to examples
8bfaa5a [Xiangrui Meng] change NaiveBayesParams to Params
fe23dcb [Xiangrui Meng] remove main from KMeans and add DenseKMeans as an example
67f4448 [Xiangrui Meng] remove main methods from linear regression algorithms and add LinearRegression example
b066bbc [Xiangrui Meng] remove main from ALS and add MovieLensALS example
b040f3b [Xiangrui Meng] change BinaryClassificationParams to Params
577945b [Xiangrui Meng] remove unused imports from NB
3d299bc [Xiangrui Meng] remove main from LR/SVM and add an example app for binary classification
f70878e [Xiangrui Meng] remove main from NaiveBayes and add an example NaiveBayes app
01ec2cd [Xiangrui Meng] Merge branch 'master' into mllib-main
9420692 [Xiangrui Meng] add scopt to examples dependencies

1, Fix SPARK-1441: compile spark core error with hadoop 0.23.x
2, Fix SPARK-1491: maven hadoop-provided profile fails to build
3, Fix org.scala-lang: * ,org.apache.avro:* inconsistent versions dependency
4, A modified on the sql/catalyst/pom.xml,sql/hive/pom.xml,sql/core/pom.xml (Four spaces formatted into two spaces)

Author: witgo <witgo@qq.com>

Closes #480 from witgo/format_pom and squashes the following commits:

03f652f [witgo] review commit
b452680 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
bee920d [witgo] revert fix SPARK-1629: Spark Core missing commons-lang dependence
7382a07 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
6902c91 [witgo] fix SPARK-1629: Spark Core missing commons-lang dependence
0da4bc3 [witgo] merge master
d1718ed [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
e345919 [witgo] add avro dependency to yarn-alpha
77fad08 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
62d0862 [witgo] Fix org.scala-lang: * inconsistent versions dependency
1a162d7 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
934f24d [witgo] review commit
cf46edc [witgo] exclude jruby
06e7328 [witgo] Merge branch 'SparkBuild' into format_pom
99464d2 [witgo] fix maven hadoop-provided profile fails to build
0c6c1fc [witgo] Fix compile spark core error with hadoop 0.23.x
6851bec [witgo] Maintain consistent SparkBuild.scala, pom.xml

sbt/sbt hive/console will fail as TestHive changed its package from "org.apache.spark.sql.hive" to "org.apache.spark.sql.hive.test".

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

Closes #574 from chenghao-intel/hive_console and squashes the following commits:

de14035 [Cheng Hao] Update the import package name for TestHive in sbt shell

It registers more Scala classes, including things like Ranges that we had to register manually before. See https://github.com/twitter/chill/releases for Chill's change log.

Author: Matei Zaharia <matei@databricks.com>

Closes #543 from mateiz/chill-0.3.6 and squashes the following commits:

a1dc5e0 [Matei Zaharia] Upgrade Chill to 0.3.6 and remove our special registration of Ranges

Updated the Flume dependency in the maven pom file and the scala build file.

Author: tmalaska <ted.malaska@cloudera.com>

Closes #507 from tmalaska/master and squashes the following commits:

79492c8 [tmalaska] excluded all thrift
159c3f1 [tmalaska] fixed the flume pom file issues
5bf56a7 [tmalaska] Upgrade flume version