## What changes were proposed in this pull request?

EdgeRDD/VertexRDD overrides checkpoint() and isCheckpointed() to forward these to the internal partitionRDD. So when checkpoint() is called on them, its the partitionRDD that actually gets checkpointed. However since isCheckpointed() also overridden to call partitionRDD.isCheckpointed, EdgeRDD/VertexRDD.isCheckpointed returns true even though this RDD is actually not checkpointed.

This would have been fine except the RDD's internal logic for computing the RDD depends on isCheckpointed(). So for VertexRDD/EdgeRDD, since isCheckpointed is true, when computing Spark tries to read checkpoint data of VertexRDD/EdgeRDD even though they are not actually checkpointed. Through a crazy sequence of call forwarding, it reads checkpoint data of partitionsRDD and tries to cast it to types in Vertex/EdgeRDD. This leads to ClassCastException.

The minimal fix that does not change any public behavior is to modify RDD internal to not use public override-able API for internal logic.
## How was this patch tested?

New unit tests.

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

Closes #15396 from tdas/SPARK-14804.

(cherry picked from commit 47d5d0dd)
Signed-off-by: Tathagata Das <tathagata.das1565@gmail.com>

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.

(cherry picked from commit afd9bc1d)
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>

## What changes were proposed in this pull request?

Currently, single line comment does not mark down backticks to `<code>..</code>` but prints as they are (`` `..` ``). For example, the line below:

```scala
/** Return an RDD with the pairs from `this` whose keys are not in `other`. */
```

So, we could work around this as below:

```scala
/**
 * Return an RDD with the pairs from `this` whose keys are not in `other`.
 */
```

- javadoc

  - **Before**
    ![2016-11-29 10 39 14](https://cloud.githubusercontent.com/assets/6477701/20693606/e64c8f90-b622-11e6-8dfc-4a029216e23d.png)

  - **After**
    ![2016-11-29 10 39 08](https://cloud.githubusercontent.com/assets/6477701/20693607/e7280d36-b622-11e6-8502-d2e21cd5556b.png)

- scaladoc (this one looks fine either way)

  - **Before**
    ![2016-11-29 10 38 22](https://cloud.githubusercontent.com/assets/6477701/20693640/12c18aa8-b623-11e6-901a-693e2f6f8066.png)

  - **After**
    ![2016-11-29 10 40 05](https://cloud.githubusercontent.com/assets/6477701/20693642/14eb043a-b623-11e6-82ac-7cd0000106d1.png

)

I suspect this is related with SPARK-16153 and genjavadoc issue in ` typesafehub/genjavadoc#85`.

## How was this patch tested?

I found them via

```
grep -r "\/\*\*.*\`" . | grep .scala
````

and then checked if each is in the public API documentation with manually built docs (`jekyll build`) with Java 7.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #16050 from HyukjinKwon/javadoc-markdown.

(cherry picked from commit 1a870090)
Signed-off-by: Sean Owen <sowen@cloudera.com>

[SPARK-3359][DOCS] Make javadoc8 working for unidoc/genjavadoc compatibility in Java API documentation

## What changes were proposed in this pull request?

This PR make `sbt unidoc` complete with Java 8.

This PR roughly includes several fixes as below:

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

  ```diff
  - * A column that will be computed based on the data in a [[DataFrame]].
  + * A column that will be computed based on the data in a `DataFrame`.
  ```

- Fix throws annotations so that they are recognisable in javadoc

- Fix URL links to `<a href="http..."></a>`.

  ```diff
  - * [[http://en.wikipedia.org/wiki/Decision_tree_learning Decision tree]] model for regression.
  + * <a href="http://en.wikipedia.org/wiki/Decision_tree_learning">
  + * Decision tree (Wikipedia)</a> model for regression.
  ```

  ```diff
  -   * see http://en.wikipedia.org/wiki/Receiver_operating_characteristic
  +   * see <a href="http://en.wikipedia.org/wiki/Receiver_operating_characteristic">
  +   * Receiver operating characteristic (Wikipedia)</a>
  ```

- Fix < to > to

  - `greater than`/`greater than or equal to` or `less than`/`less than or equal to` where applicable.

  - Wrap it with `{{{...}}}` to print them in javadoc or use `{code ...}` or `{literal ..}`. Please refer https://github.com/apache/spark/pull/16013#discussion_r89665558



- Fix `</p>` complaint

## 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)
```

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #16013 from HyukjinKwon/SPARK-3359-errors-more.

(cherry picked from commit f830bb91)
Signed-off-by: Sean Owen <sowen@cloudera.com>

[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.

(cherry picked from commit 51b1c155)
Signed-off-by: Sean Owen <sowen@cloudera.com>

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

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

)

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.

(cherry picked from commit d5b1d5fc)
Signed-off-by: Sean Owen <sowen@cloudera.com>

## What changes were proposed in this pull request?
add the param checking to keep in line with other algos

## How was this patch tested?
existing tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #15876 from zhengruifeng/param_check_runParallelPersonalizedPageRank.

(cherry picked from commit 75934457)
Signed-off-by: DB Tsai <dbtsai@dbtsai.com>

(Updated version of [PR-9457](https://github.com/apache/spark/pull/9457), rebased on latest Spark master, and using mllib-local).

This implements a parallel version of personalized pagerank, which runs all propagations for a list of source vertices in parallel.

I ran a few benchmarks on the full [DBpedia](http://dbpedia.org/) graph. When running personalized pagerank for only one source node, the existing implementation is twice as fast as the parallel one (because of the SparseVector overhead). However for 10 source nodes, the parallel implementation is four times as fast. When increasing the number of source nodes, this difference becomes even greater.

![image](https://cloud.githubusercontent.com/assets/2491/10927702/dd82e4fa-8256-11e5-89a8-4799b407f502.png)

Author: Yves Raimond <yraimond@netflix.com>

Closes #14998 from moustaki/parallel-ppr.

[SPARK-16779][TRIVIAL] Avoid using postfix operators where they do not add much and remove whitelisting

## What changes were proposed in this pull request?

Avoid using postfix operation for command execution in SQLQuerySuite where it wasn't whitelisted and audit existing whitelistings removing postfix operators from most places. Some notable places where postfix operation remains is in the XML parsing & time units (seconds, millis, etc.) where it arguably can improve readability.

## How was this patch tested?

Existing tests.

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

Closes #14407 from holdenk/SPARK-16779.

[SPARK-16694][CORE] Use for/foreach rather than map for Unit expressions whose side effects are required

## What changes were proposed in this pull request?

Use foreach/for instead of map where operation requires execution of body, not actually defining a transformation

## How was this patch tested?

Jenkins

Author: Sean Owen <sowen@cloudera.com>

Closes #14332 from srowen/SPARK-16694.

## What changes were proposed in this pull request?

I added caching in every iteration for sccGraph that is returned in strongly connected components. Without this cache strongly connected components returned graph that needed to be computed from scratch when some intermediary caches didn't existed anymore.

## How was this patch tested?
I tested it by running code similar to the one  [on databrics](https://databricks-prod-cloudfront.cloud.databricks.com/public/4027ec902e239c93eaaa8714f173bcfc/4889410027417133/3634650767364730/3117184429335832/latest.html). Basically I generated large graph  and computed strongly connected components with changed code, than simply run count on vertices and edges. Count after this update takes few seconds instead 20 minutes.

# statement
contribution is my original work and I license the work to the project under the project's open source license.

Author: Michał Wesołowski <michal.wesolowski@bzwbk.pl>

Closes #14137 from wesolowskim/SPARK-16478.

[SPARK-16535][BUILD] In pom.xml, remove groupId which is redundant definition and inherited from the parent

https://issues.apache.org/jira/browse/SPARK-16535

## What changes were proposed in this pull request?

When I scan through the pom.xml of sub projects, I found this warning as below and attached screenshot
```
Definition of groupId is redundant, because it's inherited from the parent
```
![screen shot 2016-07-13 at 3 13 11 pm](https://cloud.githubusercontent.com/assets/3925641/16823121/744f893e-4916-11e6-8a52-042f83b9db4e.png)

I've tried to remove some of the lines with groupId definition, and the build on my local machine is still ok.
```
<groupId>org.apache.spark</groupId>
```
As I just find now `<maven.version>3.3.9</maven.version>` is being used in Spark 2.x, and Maven-3 supports versionless parent elements: Maven 3 will remove the need to specify the parent version in sub modules. THIS is great (in Maven 3.1).

ref: http://stackoverflow.com/questions/3157240/maven-3-worth-it/3166762#3166762

## How was this patch tested?

I've tested by re-building the project, and build succeeded.

Author: Xin Ren <iamshrek@126.com>

Closes #14189 from keypointt/SPARK-16535.

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

## What changes were proposed in this pull request?

These are yet more changes that resolve problems with unidoc/genjavadoc and Java 8. It does not fully resolve the problem, but gets rid of as many errors as we can from this end.

## How was this patch tested?

Jenkins build of docs

Author: Sean Owen <sowen@cloudera.com>

Closes #14221 from srowen/SPARK-3359.3.

## What changes were proposed in this pull request?
After SPARK-16476 (committed earlier today as #14128), we can finally bump the version number.

## How was this patch tested?
N/A

Author: Reynold Xin <rxin@databricks.com>

Closes #14130 from rxin/SPARK-16477.

## What changes were proposed in this pull request?

There are two test data files used for graphx examples existing in directory "graphx/data"
I move it into "data/" directory because the "graphx" directory is used for code files and other test data files (such as mllib, streaming test data) are all in there.

I also update the graphx document where reference the data files which I move place.

## How was this patch tested?

N/A

Author: WeichenXu <WeichenXu123@outlook.com>

Closes #14010 from WeichenXu123/move_graphx_data_dir.

## What changes were proposed in this pull request?

`an -> a`

Use cmds like `find . -name '*.R' | xargs -i sh -c "grep -in ' an [^aeiou]' {} && echo {}"` to generate candidates, and review them one by one.

## How was this patch tested?
manual tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #13515 from zhengruifeng/an_a.

## 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.

## What changes were proposed in this pull request?

This PR removes a stale TODO comment in `GraphGenerators.scala`

## How was this patch tested?

Just comment removed.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #12839 from dongjoon-hyun/SPARK-15057.

This reverts commit dae538a4.

## What changes were proposed in this pull request?

This PR adds `since` tag into the matrix and vector classes in spark-mllib-local.

## How was this patch tested?

Scala-style checks passed.

Author: Pravin Gadakh <prgadakh@in.ibm.com>

Closes #12416 from pravingadakh/SPARK-14613.

## What changes were proposed in this pull request?

Minor typo fixes (too minor to deserve separate a JIRA)

## How was this patch tested?

local build

Author: Jacek Laskowski <jacek@japila.pl>

Closes #12469 from jaceklaskowski/minor-typo-fixes.

## What changes were proposed in this pull request?

Spark uses `NewLineAtEofChecker` rule in Scala by ScalaStyle. And, most Java code also comply with the rule. This PR aims to enforce the same rule `NewlineAtEndOfFile` by CheckStyle explicitly. Also, this fixes lint-java errors since SPARK-14465. The followings are the items.

- Adds a new line at the end of the files (19 files)
- Fixes 25 lint-java errors (12 RedundantModifier, 6 **ArrayTypeStyle**, 2 LineLength, 2 UnusedImports, 2 RegexpSingleline, 1 ModifierOrder)

## How was this patch tested?

After the Jenkins test succeeds, `dev/lint-java` should pass. (Currently, Jenkins dose not run lint-java.)
```bash
$ dev/lint-java
Using `mvn` from path: /usr/local/bin/mvn
Checkstyle checks passed.
```

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #12632 from dongjoon-hyun/SPARK-14868.