[SPARK-17173][SPARKR] R MLlib refactor, cleanup, reformat, fix deprecation in test

[felixcheung]

What changes were proposed in this pull request?

refactor, cleanup, reformat, fix deprecation in test

How was this patch tested?

unit tests, manual tests

[felixcheung]

@junyangq @mengxr @yanboliang @shivaram

[SparkQA]

Test build #64150 has finished for PR 14735 at commit d73a2c0.

• This patch fails SparkR unit tests.
• This patch merges cleanly.
• This patch adds no public classes.

[SparkQA]

Test build #64151 has finished for PR 14735 at commit 3ea30bb.

• This patch fails SparkR unit tests.
• This patch merges cleanly.
• This patch adds no public classes.

[SparkQA]

Test build #64154 has finished for PR 14735 at commit 1ef18d6.

• This patch fails SparkR unit tests.
• This patch merges cleanly.
• This patch adds no public classes.

[shivaram]

This seems a big enough change that it might be good to have a JIRA for this ?

[felixcheung]

This also tighten the signature for mllib by removing the previously unused ...:

# new in 2.0.0
"summary", signature(object = "GeneralizedLinearRegressionModel")
print.summary.GeneralizedLinearRegressionModel
"summary", signature(object = "NaiveBayesModel")
"fitted", signature(object = "KMeansModel")
"summary", signature(object = "KMeansModel")

# new in 2.1.0 only
"summary", signature(object = "IsotonicRegressionModel")
"spark.naiveBayes", signature(data = "SparkDataFrame", formula = "formula"
"summary", signature(object = "GaussianMixtureModel")

spark.survreg was updated in SPARK-16508

[SparkQA]

Test build #64157 has finished for PR 14735 at commit 30815e0.

• This patch passes all tests.
• This patch merges cleanly.
• This patch adds no public classes.

[SparkQA]

Test build #64161 has finished for PR 14735 at commit b42e10c.

• This patch passes all tests.
• This patch merges cleanly.
• This patch adds no public classes.

[mengxr]

@junyangq Could you help review this PR?

[junyangq]

align list arguments?

[SparkQA]

Test build #64198 has finished for PR 14735 at commit d727093.

• This patch passes all tests.
• This patch merges cleanly.
• This patch adds no public classes.

[felixcheung]

any more thought? I'd like to merge to facilitate more R mllib work.

[junyangq]

LGTM

[shivaram]

@felixcheung I didn't look at the code very closely, but will this change be required in branch-2.0 as well ? If so the merge might be hard to

[felixcheung]

I don't think they should be required for branch 2.0 - some part of the signature change with ... is likely good to have for consistency but those might also be "breaking" for a *.0.1 release

If we think we should - since we did make some changes like that in 2.0.0 branch - I could open a PR for the branch separately.

[shivaram]

Leaving it out of branch-2.0 sounds good to me.