SPARK-1675. Make clear whether computePrincipalComponents requires centered data

Just closing out this small JIRA, resolving with a comment change.

Author: Sean Owen <sowen@cloudera.com>

Closes #1171 from srowen/SPARK-1675 and squashes the following commits:

45ee9b7 [Sean Owen] Add simple note that data need not be centered for computePrincipalComponents
[SPARK-2342] Evaluation helper's output type doesn't conform to input ty...

The function cast doesn't conform to the intention of "Those expressions are supposed to be in the same data type, and also the return type." comment

Author: Yijie Shen <henry.yijieshen@gmail.com>

Closes #1283 from yijieshen/master and squashes the following commits:

c7aaa4b [Yijie Shen] [SPARK-2342] Evaluation helper's output type doesn't conform to input type
[SPARK-2109] Setting SPARK_MEM for bin/pyspark does not work.

Trivial fix.

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

Closes #1050 from ScrapCodes/SPARK-2109/pyspark-script-bug and squashes the following commits:

77072b9 [Prashant Sharma] Changed echos to redirect to STDERR.
13f48a0 [Prashant Sharma] [SPARK-2109] Setting SPARK_MEM for bin/pyspark does not work.
[HOTFIX] Synchronize on SQLContext.settings in tests.

Let's see if this fixes the ongoing series of test failures in a master build machine (https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT-pre-YARN/SPARK_HADOOP_VERSION=1.0.4,label=centos/81/).

pwendell marmbrus

Author: Zongheng Yang <zongheng.y@gmail.com>

Closes #1277 from concretevitamin/test-fix and squashes the following commits:

28c88bd [Zongheng Yang] Synchronize on SQLContext.settings in tests.
Streaming programming guide typos

Fix a bad Java code sample and a broken link in the streaming programming guide.

Author: Clément MATHIEU <clement@unportant.info>

Closes #1286 from cykl/streaming-programming-guide-typos and squashes the following commits:

b0908cb [Clément MATHIEU] Fix broken URL
9d3c535 [Clément MATHIEU] Spark streaming requires at least two working threads (scala version was OK)
[SPARK-1097] Workaround Hadoop conf ConcurrentModification issue

Workaround Hadoop conf ConcurrentModification issue

Author: Raymond Liu <raymond.liu@intel.com>

Closes #1273 from colorant/hadoopRDD and squashes the following commits:

994e98b [Raymond Liu] Address comments
e2cda3d [Raymond Liu] Workaround Hadoop conf ConcurrentModification issue
[SPARK-2350] Don't NPE while launching drivers

Prior to this change, we could throw a NPE if we launch a driver while another one is waiting, because removing from an iterator while iterating over it is not safe.

Author: Aaron Davidson <aaron@databricks.com>

Closes #1289 from aarondav/master-fail and squashes the following commits:

1cf1cf4 [Aaron Davidson] SPARK-2350: Don't NPE while launching drivers
[SPARK-2307][Reprise] Correctly report RDD blocks on SparkUI

**Problem.** The existing code in `ExecutorPage.scala` requires a linear scan through all the blocks to filter out the uncached ones. Every refresh could be expensive if there are many blocks and many executors.

**Solution.** The proper semantics should be the following: `StorageStatusListener` should contain only block statuses that are cached. This means as soon as a block is unpersisted by any mean, its status should be removed. This is reflected in the changes made in `StorageStatusListener.scala`.

Further, the `StorageTab` must stop relying on the `StorageStatusListener` changing a dropped block's status to `StorageLevel.NONE` (which no longer happens). This is reflected in the changes made in `StorageTab.scala` and `StorageUtils.scala`.

----------

If you have been following this chain of PRs like pwendell, you will quickly notice that this reverts the changes in #1249, which reverts the changes in #1080. In other words, we are adding back the changes from #1080, and fixing SPARK-2307 on top of those changes. Please ask questions if you are confused.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1255 from andrewor14/storage-ui-fix-reprise and squashes the following commits:

45416fa [Andrew Or] Merge branch 'master' of github.com:apache/spark into storage-ui-fix-reprise
a82ea25 [Andrew Or] Add tests for StorageStatusListener
8773b01 [Andrew Or] Update comment / minor changes
3afde3f [Andrew Or] Correctly report the number of blocks on SparkUI
SPARK-2282: Reuse PySpark Accumulator sockets to avoid crashing Spark

JIRA: https://issues.apache.org/jira/browse/SPARK-2282

This issue is caused by a buildup of sockets in the TIME_WAIT stage of TCP, which is a stage that lasts for some period of time after the communication closes.

This solution simply allows us to reuse sockets that are in TIME_WAIT, to avoid issues with the buildup of the rapid creation of these sockets.

Author: Aaron Davidson <aaron@databricks.com>

Closes #1220 from aarondav/SPARK-2282 and squashes the following commits:

2e5cab3 [Aaron Davidson] SPARK-2282: Reuse PySpark Accumulator sockets to avoid crashing Spark
[SPARK-2059][SQL] Don't throw TreeNodeException in `execution.ExplainCommand`

This is a fix for the problem revealed by PR #1265.

Currently `HiveComparisonSuite` ignores output of `ExplainCommand` since Catalyst query plan is quite different from Hive query plan. But exceptions throw from `CheckResolution` still breaks test cases. This PR catches any `TreeNodeException` and reports it as part of the query explanation.

After merging this PR, PR #1265 can also be merged safely.

For a normal query:

```
scala> hql("explain select key from src").foreach(println)
...
[Physical execution plan:]
[HiveTableScan [key#9], (MetastoreRelation default, src, None), None]
```

For a wrong query with unresolved attribute(s):

```
scala> hql("explain select kay from src").foreach(println)
...
[Error occurred during query planning: ]
[Unresolved attributes: 'kay, tree:]
[Project ['kay]]
[ LowerCaseSchema ]
[  MetastoreRelation default, src, None]
```

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

Closes #1294 from liancheng/safe-explain and squashes the following commits:

4318911 [Cheng Lian] Don't throw TreeNodeException in `execution.ExplainCommand`
[SPARK-1199][REPL] Remove VALId and use the original import style for defined classes.

This is an alternate solution to #1176.

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

Closes #1179 from ScrapCodes/SPARK-1199/repl-fix-second-approach and squashes the following commits:

820b34b [Prashant Sharma] Here we generate two kinds of import wrappers based on whether it is a class or not.
Update SQLConf.scala

use concurrent.ConcurrentHashMap instead of util.Collections.synchronizedMap

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #1272 from baishuo/master and squashes the following commits:

51ec55d [baishuo(白硕)] Update SQLConf.scala
63da043 [baishuo(白硕)] Update SQLConf.scala
36b6dbd [baishuo(白硕)] Update SQLConf.scala
864faa0 [baishuo(白硕)] Update SQLConf.scala
593096b [baishuo(白硕)] Update SQLConf.scala
7304d9b [baishuo(白硕)] Update SQLConf.scala
843581c [baishuo(白硕)] Update SQLConf.scala
1d3e4a2 [baishuo(白硕)] Update SQLConf.scala
0740f28 [baishuo(白硕)] Update SQLConf.scala
[SPARK-2059][SQL] Add analysis checks

This replaces #1263 with a test case.

Author: Reynold Xin <rxin@apache.org>
Author: Michael Armbrust <michael@databricks.com>

Closes #1265 from rxin/sql-analysis-error and squashes the following commits:

a639e01 [Reynold Xin] Added a test case for unresolved attribute analysis.
7371e1b [Reynold Xin] Merge pull request #1263 from marmbrus/analysisChecks
448c088 [Michael Armbrust] Add analysis checks
[SPARK-2234][SQL]Spark SQL basicOperators  add Except operator

Hi all,
I want to submit a Except operator in basicOperators.scala
In SQL case.SQL support two table do except operator.
select * from table1
except
select * from table2
This operator support the substract function .Return an table with the elements from `this` that are not in `other`.This operator should limit the input SparkPlan Seq only has two member.The check will later support
JIRA:https://issues.apache.org/jira/browse/SPARK-2234

Author: Yanjie Gao <gaoyanjie55@163.com>
Author: YanjieGao <396154235@qq.com>
Author: root <root@node4.(none)>
Author: gaoyanjie <gaoyanjie55@163.com>

Closes #1151 from YanjieGao/patch-6 and squashes the following commits:

f19f899 [YanjieGao] add a new blank line in basicoperators.scala
2ff7d73 [YanjieGao] resolve the identation in SqlParser and SparkStrategies
fdb5227 [YanjieGao] Merge remote branch 'upstream/master' into patch-6
9940d19 [YanjieGao] make comment less than 100c
09c7413 [YanjieGao] pr 1151 SqlParser add cache ,basic Operator rename Except and modify comment
b4b5867 [root] Merge remote branch 'upstream/master' into patch-6
b4c3869 [Yanjie Gao] change SparkStrategies Sparkcontext to SqlContext
7e0ec29 [Yanjie Gao] delete multi test
7e7c83f [Yanjie Gao] delete conflict except
b01beb8 [YanjieGao] resolve conflict sparkstrategies and basicOperators
4dc8166 [YanjieGao] resolve conflict
fa68a98 [Yanjie Gao] Update joins.scala
8e6bb00 [Yanjie Gao] delete conflict except
dd9ba5e [Yanjie Gao] Update joins.scala
a0d4e73 [Yanjie Gao] delete skew join
60f5ddd [Yanjie Gao] update less than 100c
0e72233 [Yanjie Gao] update SQLQuerySuite on master branch
7f916b5 [Yanjie Gao] update execution/basicOperators on master branch
a28dece [Yanjie Gao] Update logical/basicOperators on master branch
a639935 [Yanjie Gao] Update SparkStrategies.scala
3bf7def [Yanjie Gao] update SqlParser on master branch
26f833f [Yanjie Gao] update SparkStrategies.scala on master branch
8dd063f [Yanjie Gao] Update logical/basicOperators on master branch
9847dcf [Yanjie Gao] update SqlParser on masterbranch
d6a4604 [Yanjie Gao] Update joins.scala
424c507 [Yanjie Gao] Update joins.scala
7680742 [Yanjie Gao] Update SqlParser.scala
a7193d8 [gaoyanjie] [SPARK-2234][SQL]Spark SQL basicOperators add Except operator #1151
5c8a224 [Yanjie Gao] update the line less than 100c
ee066b3 [Yanjie Gao] Update basicOperators.scala
32a80ab [Yanjie Gao] remove except in HiveQl
cf232eb [Yanjie Gao] update 1comment 2space3 left.out
f1ea3f3 [Yanjie Gao] remove comment
7ea9b91 [Yanjie Gao] remove annotation
7f3d613 [Yanjie Gao] update .map(_.copy())
670a1bb [Yanjie Gao] Update HiveQl.scala
3fe7746 [Yanjie Gao] Update SQLQuerySuite.scala
a36eb0a [Yanjie Gao] Update basicOperators.scala
7859e56 [Yanjie Gao] Update SparkStrategies.scala
052346d [Yanjie Gao] Subtract is conflict with Subtract(e1,e2)
aab3785 [Yanjie Gao] Update SQLQuerySuite.scala
4bf80b1 [Yanjie Gao] update subtract to except
4bdd520 [Yanjie Gao] Update SqlParser.scala
2d4bfbd [Yanjie Gao] Update SQLQuerySuite.scala
0808921 [Yanjie Gao] SQLQuerySuite
a8a1948 [Yanjie Gao] SparkStrategies
1fe96c0 [Yanjie Gao] HiveQl.scala update
3305e40 [Yanjie Gao] SqlParser
7a98c37 [Yanjie Gao] Update basicOperators.scala
cf5b9d0 [Yanjie Gao] Update basicOperators.scala
8945835 [Yanjie Gao] object SkewJoin extends Strategy
2b98962 [Yanjie Gao] Update SqlParser.scala
dd32980 [Yanjie Gao] update1
68815b2 [Yanjie Gao] Reformat the code style
4eb43ec [Yanjie Gao] Update basicOperators.scala
aa06072 [Yanjie Gao] Reformat the code sytle
HOTFIX: Clean before building docs during release.

If the docs are built after a Maven build has finished the intermediate
state somehow causes a compiler bug during sbt compilation. This just
does a clean before attempting to build the docs.
Added SignalLogger to HistoryServer.

This was omitted in #1260. @aarondav

Author: Reynold Xin <rxin@apache.org>

Closes #1300 from rxin/historyServer and squashes the following commits:

af720a3 [Reynold Xin] Added SignalLogger to HistoryServer.
[SPARK-2370][SQL] Decrease metadata retrieved for partitioned hive queries.

Author: Michael Armbrust <michael@databricks.com>

Closes #1305 from marmbrus/usePrunerPartitions and squashes the following commits:

744aa20 [Michael Armbrust] Use getAllPartitionsForPruner instead of getPartitions, which avoids retrieving auth data
[SPARK-2306]:BoundedPriorityQueue is private and not registered with Kry...

Due to the non registration of BoundedPriorityQueue  with kryoserializer, operations which are dependend on BoundedPriorityQueue are giving exceptions.One such instance is using top along with kryo serialization.
Fixed the issue by registering BoundedPriorityQueue with kryoserializer.

Author: ankit.bhardwaj <ankit.bhardwaj@guavus.com>

Closes #1299 from AnkitBhardwaj12/BoundedPriorityQueueWithKryoIssue and squashes the following commits:

a4ae8ed [ankit.bhardwaj] [SPARK-2306]:BoundedPriorityQueue is private and not registered with Kryo
[SPARK-2366] [SQL] Add column pruning for the right side of LeftSemi join.

The right side of `LeftSemi` join needs columns only used in join condition.

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

Closes #1301 from ueshin/issues/SPARK-2366 and squashes the following commits:

7677a39 [Takuya UESHIN] Update comments.
786d3a0 [Takuya UESHIN] Rename method name.
e0957b1 [Takuya UESHIN] Add column pruning for the right side of LeftSemi join.
[SPARK-2327] [SQL] Fix nullabilities of Join/Generate/Aggregate.

Fix nullabilities of `Join`/`Generate`/`Aggregate` because:
- Output attributes of opposite side of `OuterJoin` should be nullable.
- Output attributes of generater side of `Generate` should be nullable if `join` is `true` and `outer` is `true`.
- `AttributeReference` of `computedAggregates` of `Aggregate` should be the same as `aggregateExpression`'s.

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

Closes #1266 from ueshin/issues/SPARK-2327 and squashes the following commits:

3ace83a [Takuya UESHIN] Add withNullability to Attribute and use it to change nullabilities.
df1ae53 [Takuya UESHIN] Modify nullabilize to leave attribute if not resolved.
799ce56 [Takuya UESHIN] Add nullabilization to Generate of SparkPlan.
a0fc9bc [Takuya UESHIN] Fix scalastyle errors.
0e31e37 [Takuya UESHIN] Fix Aggregate resultAttribute nullabilities.
09532ec [Takuya UESHIN] Fix Generate output nullabilities.
f20f196 [Takuya UESHIN] Fix Join output nullabilities.