[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user shivaram commented on the issue: https://github.com/apache/spark/pull/14705 I cherry-picked this PR into `branch-2.0` in https://github.com/apache/spark/commit/0297896119e11f23da4b14f62f50ec72b5fac57f -- The merge was a little awkward and but I think I got it to work correctly. The CRAN checks look fine to me locally, but it would be good if somebody else can also verify this. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 Thanks. Reviewing each change, I think we need this PR (14705) and PR #14734 in 2.0.1 - so maybe only a few lines of conflicts. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user shivaram commented on the issue: https://github.com/apache/spark/pull/14705 Yeah so we can do a couple of things. One is we try to cherry-pick this PR to branch-2.0 and then fix all the merge conflicts that are thrown. I think that should handle cases where the method doesn't exist in 2.0 etc. The other option is to create a new PR that is targeted at branch-2.0 (i.e. the cherry-pick / merge can be done as a part of development) and then we can review, merge it. Let me know if you or @junyangq want to try the second option -- If not I can try the first one and see how many conflicts there are. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 I think a subset of this should go to 2.0.1 as well (as requirement to fix warning for CRAN in 2.0.x), but it's a non-trivial port: mllib isoreg are new in 2.1.0 only. What's the best way to proceed? --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user junyangq commented on the issue: https://github.com/apache/spark/pull/14705 Thanks @felixcheung! --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 Yes agreed. I will do one more pass tonight and merge if there isn't any blocking issue. Thanks! --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user mengxr commented on the issue: https://github.com/apache/spark/pull/14705 Agree with @felixcheung . Let do the `setGeneric(, ...)` and do not use `...` in function definition if it is not required. Note that having every param documented is not a strict requirement of CRAN submission. It would be great if we can merge this PR fist and fix minor issues after since it touches many files in SparkR. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user junyangq commented on the issue: https://github.com/apache/spark/pull/14705 That makes sense. Perhaps this could be done in another PR? --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 I think it's ok to put @param ... on top of the function in the order we want it. Or @param na.rm for sd, var etc. Yes it is a bit odd to have param in the documentation block that is not in the immediate signature, but to me it seems better than making the API contract weaker just so we could document it (or get some warnings to go away). We could consider this as you need to include both function definition and generic definition for documentation and the place to do that is on top of the function definition (which is just for maintainability and convenient). Other packages have opted to maintain separate Rd files which could have other issues. I don't want to drag this PR on though. We could address the warnings now and revisit later - I am concerned with adding params to function signature that weaken it. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user junyangq commented on the issue: https://github.com/apache/spark/pull/14705 Yeah, I totally agree that in terms of usage this is safer. Then the doc for `...` would be an issue. If we keep to the principle that doc be close to the function, then `...` would be in generic part. That seems not what we want to do. Putting it above the function definition is also a little weird since there is not `...` in the arguments of the function itself. No sure which is the best way though... --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/14705
Hmm, I'm beginning to think we could do this:
```
generics.R
setGeneric("spark.naiveBayes", function(data, formula, ...) {
standardGeneric("spark.naiveBayes") })
```
```
mllib.R
#' @param ... additional argument(s) passed to the method. Currently only
\code{smoothing}.
setMethod("spark.naiveBayes", signature(data = "SparkDataFrame", formula =
"formula"),
function(data, formula, smoothing = 1.0) {
# note, no `...`
```
That we wouldn't need `...` in the function definition?
I'd argue this because:
```
> a <- function(correct, ...) { print("foo") }
> a(correct = "a", wrong = "b")
[1] "foo"
> a(correcy = "b")
[1] "foo"
# versus
> a <- function(correct) { print("foo") }
> a(correcy = "b")
Error in a(correcy = "b") : unused argument (correcy = "b")
> a(wrong = "b")
Error in a(wrong = "b") : unused argument (wrong = "b")
```
With `...` in the function definition, typo or misuse would not be detected
easily.
Would that be better off? what do you think?
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[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
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Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 surely - we should have said `lint-r` as the baseline. There's definitely more we could add though. It would be great if we have bandwidth to write more [linters](https://github.com/jimhester/lintr/blob/master/vignettes/creating_linters.Rmd) at some point. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user HyukjinKwon commented on the issue: https://github.com/apache/spark/pull/14705 @felixcheung Thanks for kind explanation. BTW, it'd be great too if it just has a sentence, for example, `"For R code, Apache Spark follows lint-r"` in the wiki just like Python has `"For Python code, Apache Spark follows PEP 8 with one exception: lines can be up to 100 characters in length, not 79."` for just correctness and references for new contributors if it makes any sense maybe :). --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 looking good - looks like we are very close. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 @inheritParams would be the way to go. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user felixcheung commented on the issue: https://github.com/apache/spark/pull/14705 @HyukjinKwon - we don't have a coding style guide for R. We have some style check with lint-r. In addition, the document style you are looking at is a bit different from coding style - this document style I'm planning to write one after this is merged. Perhaps a coding style could be good too, for things like eg. "what to do with method without parameter". --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user junyangq commented on the issue: https://github.com/apache/spark/pull/14705 @shivaram I found perhaps a neat way to document R'glm if we don't want to remove it is to use `@inheritParams stats::glm`. That will bring in all the parameters from `stats::glm` not listed in SparkR's glm. That also means we need slight modification of the `data` description: something like "a SparkDataFrame or R's glm data for training." --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user HyukjinKwon commented on the issue: https://github.com/apache/spark/pull/14705 @shivaram BTW do you mind if I ask if we have R style guidelines somewhere please? I remember I made a PR for R referencing only the other codes. It seems it is also missing in https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user shivaram commented on the issue: https://github.com/apache/spark/pull/14705 Yeah I think we will be more careful about adding new algorithms to override existing R methods -- but given that `glm` is already exposed I'd think we can make an exception for just this one. @mengxr Any thoughts on this ? --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
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Github user junyangq commented on the issue: https://github.com/apache/spark/pull/14705 I don't have a good answer in mind now. I'm not sure how much we gain by making `glm` also applicable to `SparkDataFrame` as well. Would `spark.glm` be enough, like other ML methods? --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
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[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user shivaram commented on the issue: https://github.com/apache/spark/pull/14705 Thanks @junyangq -- I just ran the check on `branch-2.0` with this PR and in addition to `glm` there were two warnings for `...` in `first` and `unpersist` that we can fix in this PR. For `glm` its kind of unfortunate but I think we need to just go ahead and add those args and say that those are not used by SparkR. Is there any other workaround you have in mind ? We can do that in a separate PR if required. ``` Undocumented arguments in documentation object 'first' â...â Undocumented arguments in documentation object 'glm' âweightsâ âsubsetâ âna.actionâ âstartâ âetastartâ âmustartâ âoffsetâ âcontrolâ âmodelâ âmethodâ âxâ âyâ âcontrastsâ â...â Undocumented arguments in documentation object 'unpersist' â...â ``` --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user AmplabJenkins commented on the issue: https://github.com/apache/spark/pull/14705 Merged build finished. Test PASSed. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user SparkQA commented on the issue: https://github.com/apache/spark/pull/14705 **[Test build #64015 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64015/consoleFull)** for PR 14705 at commit [`8d60676`](https://github.com/apache/spark/commit/8d606763fa3ebca8f7657384313f7805a3b086ad). * This patch passes all tests. * This patch merges cleanly. * This patch adds no public classes. --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
[GitHub] spark issue #14705: [SPARK-16508][SparkR] Fix CRAN undocumented/duplicated a...
Github user SparkQA commented on the issue: https://github.com/apache/spark/pull/14705 **[Test build #64015 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64015/consoleFull)** for PR 14705 at commit [`8d60676`](https://github.com/apache/spark/commit/8d606763fa3ebca8f7657384313f7805a3b086ad). --- If your project is set up for it, you can reply to this email and have your reply appear on GitHub as well. If your project does not have this feature enabled and wishes so, or if the feature is enabled but not working, please contact infrastructure at infrastruct...@apache.org or file a JIRA ticket with INFRA. --- - To unsubscribe, e-mail: reviews-unsubscr...@spark.apache.org For additional commands, e-mail: reviews-h...@spark.apache.org
