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Posted to reviews@spark.apache.org by felixcheung <gi...@git.apache.org> on 2017/10/23 07:21:44 UTC
[GitHub] spark pull request #19557: [SPARK-22281][SPARKR] Handle R method breaking si...
GitHub user felixcheung opened a pull request:
https://github.com/apache/spark/pull/19557
[SPARK-22281][SPARKR] Handle R method breaking signature changes
## What changes were proposed in this pull request?
This is to fix the code for the latest R changes in R-devel
```
hecking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'attach':
attach
Code: function(what, pos = 2L, name = deparse(substitute(what),
backtick = FALSE), warn.conflicts = TRUE)
Docs: function(what, pos = 2L, name = deparse(substitute(what)),
warn.conflicts = TRUE)
Mismatches in argument default values:
Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs: deparse(substitute(what))
Codoc mismatches from documentation object 'glm':
glm
Code: function(formula, family = gaussian, data, weights, subset,
na.action, start = NULL, etastart, mustart, offset,
control = list(...), model = TRUE, method = "glm.fit",
x = FALSE, y = TRUE, singular.ok = TRUE, contrasts =
NULL, ...)
Docs: function(formula, family = gaussian, data, weights, subset,
na.action, start = NULL, etastart, mustart, offset,
control = list(...), model = TRUE, method = "glm.fit",
x = FALSE, y = TRUE, contrasts = NULL, ...)
Argument names in code not in docs:
singular.ok
Mismatches in argument names:
Position: 16 Code: singular.ok Docs: contrasts
Position: 17 Code: contrasts Docs: ...
```
With attach, we need to match the signature of base::attach, since it changes we are going to generate the signature at runtime by pulling from base::attach directly.
With glm it's pulling in the function definition (ie. "usage") from the stats::glm function. Since this is "compiled in" when we build the source package into the .Rd file, when it changes at runtime or in CRAN check it won't match the latest signature. The solution is not to pull in from stats::glm since there isn't much value in doing that (none of the param we actually use, the ones we do use we have explicitly documented them)
## How was this patch tested?
Manually.
- [ ] check on other platform, r-hub, on r-devel etc..
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rattachglmdocerror
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/19557.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 #19557
----
commit 7b145bac854851e4a87935c80b3688513eb58cb7
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-10-23T07:17:43Z
fix attach and glm
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[GitHub] spark pull request #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaki...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/19557#discussion_r146757193
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3249,9 +3249,12 @@ setMethod("as.data.frame",
#' @note attach since 1.6.0
setMethod("attach",
signature(what = "SparkDataFrame"),
- function(what, pos = 2, name = deparse(substitute(what)), warn.conflicts = TRUE) {
- newEnv <- assignNewEnv(what)
- attach(newEnv, pos = pos, name = name, warn.conflicts = warn.conflicts)
+ function(what, pos = 2L, name = deparse(substitute(what), backtick = FALSE),
+ warn.conflicts = TRUE) {
+ args <- as.list(environment()) # capture all parameters - this must be the first line
+ newEnv <- assignNewEnv(args$what)
+ args$what <- newEnv
+ do.call(attach, args)
--- End diff --
calling attach this way to avoid it getting flagged...
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[GitHub] spark pull request #19557: [SPARK-22281][SPARKR] Handle R method breaking si...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/19557#discussion_r146182283
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3247,12 +3247,23 @@ setMethod("as.data.frame",
#' }
#' @seealso \link{detach}
#' @note attach since 1.6.0
-setMethod("attach",
- signature(what = "SparkDataFrame"),
- function(what, pos = 2, name = deparse(substitute(what)), warn.conflicts = TRUE) {
- newEnv <- assignNewEnv(what)
- attach(newEnv, pos = pos, name = name, warn.conflicts = warn.conflicts)
- })
+#' @name attach
+NULL
+
+createAttachMethod <- function() {
+ f <- function() {
+ args <- as.list(environment()) # capture all function parameters - this must be the first line
+ newEnv <- assignNewEnv(args$what)
+ args$what <- newEnv
+ do.call(attach, args)
--- End diff --
since I'm changing to `do.call` - so that we can retain the param name/value order without having to hardcode them here - we are no longer being flagged with the NOTE on calling `attach` :)
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[GitHub] spark pull request #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaki...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/19557#discussion_r146757169
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3249,9 +3249,12 @@ setMethod("as.data.frame",
#' @note attach since 1.6.0
setMethod("attach",
signature(what = "SparkDataFrame"),
- function(what, pos = 2, name = deparse(substitute(what)), warn.conflicts = TRUE) {
- newEnv <- assignNewEnv(what)
- attach(newEnv, pos = pos, name = name, warn.conflicts = warn.conflicts)
+ function(what, pos = 2L, name = deparse(substitute(what), backtick = FALSE),
+ warn.conflicts = TRUE) {
--- End diff --
changing this to match the latest R-devel param signature
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[GitHub] spark pull request #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaki...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/19557#discussion_r146772862
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3249,9 +3249,12 @@ setMethod("as.data.frame",
#' @note attach since 1.6.0
setMethod("attach",
signature(what = "SparkDataFrame"),
- function(what, pos = 2, name = deparse(substitute(what)), warn.conflicts = TRUE) {
- newEnv <- assignNewEnv(what)
- attach(newEnv, pos = pos, name = name, warn.conflicts = warn.conflicts)
+ function(what, pos = 2L, name = deparse(substitute(what), backtick = FALSE),
+ warn.conflicts = TRUE) {
--- End diff --
this will need to be updated manually...
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19557
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR] Handle R method breaking signature...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19557
rebased
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
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Posted by asfgit <gi...@git.apache.org>.
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR] Handle R method breaking signature...
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR] Handle R method breaking signature...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19557
LGTM.
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19557
unfortunately `attach` part didn't work on r-devel.
I think you are right, I'm going try to apply the similar approach for `attach` - i started that way before I found out method signature was not the cause for `glm`. So now I'm going backtrack to re-do `attach` too.
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[GitHub] spark pull request #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaki...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/19557#discussion_r146760035
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3249,9 +3249,12 @@ setMethod("as.data.frame",
#' @note attach since 1.6.0
setMethod("attach",
signature(what = "SparkDataFrame"),
- function(what, pos = 2, name = deparse(substitute(what)), warn.conflicts = TRUE) {
- newEnv <- assignNewEnv(what)
- attach(newEnv, pos = pos, name = name, warn.conflicts = warn.conflicts)
+ function(what, pos = 2L, name = deparse(substitute(what), backtick = FALSE),
+ warn.conflicts = TRUE) {
--- End diff --
So this is the only thing we might need to update if R changes something ? Also how does this keep working with the older R version as well
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
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Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19557
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR] Handle R method breaking signature...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19557
Is there a reason we can't use the same glm trick for attach ? I guess this was explained above but I'm wondering if there is a reason the base::attach is not compiled in the same way ?
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR] Handle R method breaking signature...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
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merged to master/2.2
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[GitHub] spark pull request #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaki...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/19557#discussion_r146757250
--- Diff: R/run-tests.sh ---
@@ -38,6 +38,7 @@ FAILED=$((PIPESTATUS[0]||$FAILED))
NUM_CRAN_WARNING="$(grep -c WARNING$ $CRAN_CHECK_LOG_FILE)"
NUM_CRAN_ERROR="$(grep -c ERROR$ $CRAN_CHECK_LOG_FILE)"
NUM_CRAN_NOTES="$(grep -c NOTE$ $CRAN_CHECK_LOG_FILE)"
+HAS_PACKAGE_VERSION_WARN="$(grep -c "Insufficient package version" $CRAN_CHECK_LOG_FILE)"
--- End diff --
changes to this file is from the other PR plus one change to $NUM_CRAN_NOTES - 1
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19557
well, this change avoided the warning but disabled help too (which is probably why it's working)
```
> showMethods("attach")
Function: attach (package base)
what="ANY"
what="SparkDataFrame"
> showMethods("fitted")
Function: fitted (package stats)
object="ANY"
object="BisectingKMeansModel"
object="KMeansModel"
> ?fitted
Help on topic ‘fitted’ was found in the following packages:
Package Library
SparkR /opt/spark-2.3.0-bin-hadoop2.7/R/lib
stats /usr/lib/R/library
Choose one
1: Get fitted result from a k-means model {SparkR}
2: Extract Model Fitted Values {stats}
Selection: 0
> ?attach
> ?SparkR::fitted
> ?SparkR::attach
No documentation for ‘attach’ in specified packages and libraries:
you could try ‘??attach’
```
basically it shows without asking the base::attach, `?SparkR::attach` doesn't work either
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19557
@felixcheung Are the docs on this version good ?
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
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tested on windows, r-hub/r-devel
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19557
Yes I just tested this with r-hub on r-devel and release.
I will test a couple more things but this is looking good.
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19557
Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/83038/
Test PASSed.
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[GitHub] spark issue #19557: [SPARK-22281][SPARKR][WIP] Handle R method breaking sign...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19557
**[Test build #83038 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/83038/testReport)** for PR 19557 at commit [`8f84aa6`](https://github.com/apache/spark/commit/8f84aa6bdf5df174adc52fc6025d2fdbcd2d27de).
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