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Posted to reviews@spark.apache.org by felixcheung <gi...@git.apache.org> on 2016/08/20 16:20:56 UTC
[GitHub] spark pull request #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reform...
GitHub user felixcheung opened a pull request:
https://github.com/apache/spark/pull/14735
[MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix deprecation in test
## What changes were proposed in this pull request?
refactor, cleanup, reformat, fix deprecation in test
## How was this patch tested?
unit tests, manual tests
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rmllibutil
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/14735.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #14735
----
commit d73a2c04ef3ba0cc033f79d4c83e8dd659f71b47
Author: Felix Cheung <fe...@hotmail.com>
Date: 2016-08-20T16:14:19Z
refactor, cleanup, fix deprecation in test
----
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by junyangq <gi...@git.apache.org>.
Github user junyangq commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75598531
--- Diff: R/pkg/R/mllib.R ---
@@ -1052,8 +1034,8 @@ setMethod("summary", signature(object = "GaussianMixtureModel"),
} else {
dataFrame(callJMethod(jobj, "posterior"))
}
- return(list(lambda = lambda, mu = mu, sigma = sigma,
- posterior = posterior, is.loaded = is.loaded))
+ list(lambda = lambda, mu = mu, sigma = sigma,
+ posterior = posterior, is.loaded = is.loaded)
--- End diff --
alignment?
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by junyangq <gi...@git.apache.org>.
Github user junyangq commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75599753
--- Diff: R/pkg/inst/tests/testthat/test_mllib.R ---
@@ -95,6 +95,10 @@ test_that("spark.glm summary", {
expect_equal(stats$df.residual, rStats$df.residual)
expect_equal(stats$aic, rStats$aic)
+ out <- capture.output(print(stats))
+ expect_match(out[2], "Deviance Residuals:")
+ expect_true(any(grepl("AIC: 59.22", out)))
--- End diff --
Are we trying to test `print.summary.GeneralizedLinearRegressionModel` function here?
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/14735
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75638333
--- Diff: R/pkg/R/mllib.R ---
@@ -499,11 +505,11 @@ setMethod("predict", signature(object = "IsotonicRegressionModel"),
#' @export
#' @note summary(IsotonicRegressionModel) since 2.1.0
setMethod("summary", signature(object = "IsotonicRegressionModel"),
- function(object, ...) {
--- End diff --
The annotation ```@param ... Other optional arguments to summary of an IsotonicRegressionModel``` is not be used and should be removed?
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the issue:
https://github.com/apache/spark/pull/14735
@junyangq Could you help review this PR?
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/14735
This also tighten the signature for mllib by removing the previously unused `...`:
```
"summary", signature(object = "GeneralizedLinearRegressionModel")
print.summary.GeneralizedLinearRegressionModel
"summary", signature(object = "NaiveBayesModel")
"summary", signature(object = "IsotonicRegressionModel")
"fitted", signature(object = "KMeansModel")
"summary", signature(object = "KMeansModel")
"spark.naiveBayes", signature(data = "SparkDataFrame", formula = "formula"
"summary", signature(object = "GaussianMixtureModel")
```
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75661739
--- Diff: R/pkg/R/mllib.R ---
@@ -499,11 +505,11 @@ setMethod("predict", signature(object = "IsotonicRegressionModel"),
#' @export
#' @note summary(IsotonicRegressionModel) since 2.1.0
setMethod("summary", signature(object = "IsotonicRegressionModel"),
- function(object, ...) {
--- End diff --
ditto.
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14735
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14735
Leaving it out of branch-2.0 sounds good to me.
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14735
**[Test build #64198 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64198/consoleFull)** for PR 14735 at commit [`d727093`](https://github.com/apache/spark/commit/d727093092514f4e49f0a2f2e0814ef5df4c71ed).
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14735
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/14735
any more thought? I'd like to merge to facilitate more R mllib work.
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14735
**[Test build #64150 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64150/consoleFull)** for PR 14735 at commit [`d73a2c0`](https://github.com/apache/spark/commit/d73a2c04ef3ba0cc033f79d4c83e8dd659f71b47).
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14735
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14735
@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
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by junyangq <gi...@git.apache.org>.
Github user junyangq commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75598536
--- Diff: R/pkg/R/mllib.R ---
@@ -1163,17 +1145,17 @@ setMethod("spark.als", signature(data = "SparkDataFrame"),
#' @export
#' @note summary(ALSModel) since 2.1.0
setMethod("summary", signature(object = "ALSModel"),
-function(object, ...) {
- jobj <- object@jobj
- user <- callJMethod(jobj, "userCol")
- item <- callJMethod(jobj, "itemCol")
- rating <- callJMethod(jobj, "ratingCol")
- userFactors <- dataFrame(callJMethod(jobj, "userFactors"))
- itemFactors <- dataFrame(callJMethod(jobj, "itemFactors"))
- rank <- callJMethod(jobj, "rank")
- return(list(user = user, item = item, rating = rating, userFactors = userFactors,
- itemFactors = itemFactors, rank = rank))
-})
+ function(object) {
+ jobj <- object@jobj
+ user <- callJMethod(jobj, "userCol")
+ item <- callJMethod(jobj, "itemCol")
+ rating <- callJMethod(jobj, "ratingCol")
+ userFactors <- dataFrame(callJMethod(jobj, "userFactors"))
+ itemFactors <- dataFrame(callJMethod(jobj, "itemFactors"))
+ rank <- callJMethod(jobj, "rank")
+ list(user = user, item = item, rating = rating, userFactors = userFactors,
+ itemFactors = itemFactors, rank = rank)
--- End diff --
same as above..
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14735
**[Test build #64151 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64151/consoleFull)** for PR 14735 at commit [`3ea30bb`](https://github.com/apache/spark/commit/3ea30bb3b5d22626f6de6e0699504180f267dfdc).
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75636716
--- Diff: R/pkg/R/mllib.R ---
@@ -1027,7 +1009,7 @@ setMethod("spark.gaussianMixture", signature(data = "SparkDataFrame", formula =
#' @export
#' @note summary(GaussianMixtureModel) since 2.1.0
setMethod("summary", signature(object = "GaussianMixtureModel"),
- function(object, ...) {
--- End diff --
Then annotation ```@param ... currently not used argument(s) passed to the method.``` is not used?
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14735
Merged build finished. Test FAILed.
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by junyangq <gi...@git.apache.org>.
Github user junyangq commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75598520
--- Diff: R/pkg/R/mllib.R ---
@@ -610,8 +616,8 @@ setMethod("summary", signature(object = "KMeansModel"),
} else {
dataFrame(callJMethod(jobj, "cluster"))
}
- return(list(coefficients = coefficients, size = size,
- cluster = cluster, is.loaded = is.loaded))
+ list(coefficients = coefficients, size = size,
+ cluster = cluster, is.loaded = is.loaded)
--- End diff --
align list arguments?
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14735
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14735
**[Test build #64154 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64154/consoleFull)** for PR 14735 at commit [`1ef18d6`](https://github.com/apache/spark/commit/1ef18d6abfe854c95e0323a406065d9ee4f11c15).
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14735
This seems a big enough change that it might be good to have a JIRA for this ?
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75661714
--- Diff: R/pkg/R/mllib.R ---
@@ -1027,7 +1009,7 @@ setMethod("spark.gaussianMixture", signature(data = "SparkDataFrame", formula =
#' @export
#' @note summary(GaussianMixtureModel) since 2.1.0
setMethod("summary", signature(object = "GaussianMixtureModel"),
- function(object, ...) {
--- End diff --
It's in the generic defined in a different file generics.R
We have discussed this at length, this is unfortunately a compromise we need to take at this point. We are going to see some documentation tags spread a bit from now on.
Long story short, CRAN checks warn about undocumented parameter; we need to have the generic with `...` to match the base::summary signature; we shouldn't add `...` in the actual definition since we don't use it and having it weakens the function contract (which is discouraged).
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14735
**[Test build #64157 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64157/consoleFull)** for PR 14735 at commit [`30815e0`](https://github.com/apache/spark/commit/30815e067a37175e0f5d4539c80db6b0ec6cc159).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14735
**[Test build #64151 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64151/consoleFull)** for PR 14735 at commit [`3ea30bb`](https://github.com/apache/spark/commit/3ea30bb3b5d22626f6de6e0699504180f267dfdc).
* This patch **fails SparkR unit tests**.
* This patch merges cleanly.
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
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* This patch passes all tests.
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by junyangq <gi...@git.apache.org>.
Github user junyangq commented on the issue:
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LGTM
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[GitHub] spark issue #14735: [MINOR][SPARKR] R MLlib refactor, cleanup, reformat, fix...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/14735
@junyangq @mengxr @yanboliang @shivaram
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
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[GitHub] spark pull request #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, ...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/14735#discussion_r75664196
--- Diff: R/pkg/R/mllib.R ---
@@ -1027,7 +1009,7 @@ setMethod("spark.gaussianMixture", signature(data = "SparkDataFrame", formula =
#' @export
#' @note summary(GaussianMixtureModel) since 2.1.0
setMethod("summary", signature(object = "GaussianMixtureModel"),
- function(object, ...) {
--- End diff --
Thanks for clarification.
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by SparkQA <gi...@git.apache.org>.
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**[Test build #64161 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64161/consoleFull)** for PR 14735 at commit [`b42e10c`](https://github.com/apache/spark/commit/b42e10c84f122774411e6d9bdc08b27951161272).
* This patch passes all tests.
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[GitHub] spark issue #14735: [SPARK-17173][SPARKR] R MLlib refactor, cleanup, reforma...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/14735
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.
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* This patch **fails SparkR unit tests**.
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