[SPARK-8952] [SPARKR] - Wrap normalizePath calls with suppressWarnings

[lresende]

This is based on @davies comment on SPARK-8952 which suggests to only call normalizePath() when path starts with '~'

[shivaram]

Jenkins, ok to test

[SparkQA]

Test build #41337 has finished for PR 8343 at commit 229a8df.

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

[shivaram]

The change looks fine to me, but I am not sure we reached a consensus on the JIRA. The main problem is that right now normalizePath also handles relative paths and we'll lose that functionality with this change. So I'm not sure if this is the right fix yet -- it would be great if we could differentiate and handle local paths and HDFS paths.

Also a minor procedural point --- Could you title the pull request [SPARKR] [SPARK-8952] ... ? https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark has more details that might help.

[sun-rui]

For a short term solution, I think we can just use suppressWarnings(normalizePath(path)) to suppress the warning as is done in other places.

For a long term solution, we need to discuss if we really need this helping feature to normalize a path, as there is no such feature in Scala API. If we want this, need to differentiate and handle local paths and HDFS paths.

[lresende]

Thanks for the comments @shivaram and @sun-rui. I have standardized in using supressWarnings for all invocations of normalizePath.

[SparkQA]

Test build #41709 has finished for PR 8343 at commit f529bef.

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

[SparkQA]

Test build #41715 has finished for PR 8343 at commit 472c767.

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

[shivaram]

Thanks @lresende -- LGTM

[shivaram]

Jenkins, retest this please

[shivaram]

@lresende I'm just retesting this as we merged a R style checker. I'm sure this PR should be fine, but just want to run this through to make sure things are working fine.

FYI @yu-iskw

[shivaram]

@yu-iskw I actually an error in Jenkins which says. I guess this is from the PR that added na.omit to the NAMESPACE yesterday

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'na.omit' for signature '"integer"'
Calls: lint_package ... ends -> as.igraph.es -> inherits -> na.omit -> <Anonymous>

[yu-iskw]

@shivaram I see. I'll investigate the cause. Thank you for letting me know.

[shivaram]

I think I found the problem. Our setGeneric for na.omit is wrong. It is being too restrictive. We need a diff which looks like

-           function(x, how = c("any", "all"), minNonNulls = NULL, cols = NULL) {
+           function(object, ...) {

I'll send a PR in a minute

[SparkQA]

Test build #41718 has finished for PR 8343 at commit 472c767.

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

[shivaram]

Jenkins, retest this please

[SparkQA]

Test build #41735 has finished for PR 8343 at commit 472c767.

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

[shivaram]

lint-r looks fine, Merging this.