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Posted to reviews@spark.apache.org by felixcheung <gi...@git.apache.org> on 2016/06/13 06:38:14 UTC
[GitHub] spark pull request #13636: [SPARK-15637][SPARKR] Remove R version check sinc...
GitHub user felixcheung opened a pull request:
https://github.com/apache/spark/pull/13636
[SPARK-15637][SPARKR] Remove R version check since masked functions are fixed
## What changes were proposed in this pull request?
Because of the fix in SPARK-15684, this exclusion is no longer necessary.
## How was this patch tested?
unit tests
@shivaram
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rendswith
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/13636.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 #13636
----
commit a5eb3daeb1d34e082e22176fd272dbe49398aaa8
Author: Felix Cheung <fe...@hotmail.com>
Date: 2016-06-13T06:35:47Z
update test
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60386 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60386/consoleFull)** for PR 13636 at commit [`a5eb3da`](https://github.com/apache/spark/commit/a5eb3daeb1d34e082e22176fd272dbe49398aaa8).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R versi...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/13636#discussion_r67019739
--- Diff: R/pkg/inst/tests/testthat/test_context.R ---
@@ -19,21 +19,25 @@ context("test functions in sparkR.R")
test_that("Check masked functions", {
# Check that we are not masking any new function from base, stats, testthat unexpectedly
- masked <- conflicts(detail = TRUE)$`package:SparkR`
- expect_true("describe" %in% masked) # only when with testthat..
- func <- lapply(masked, function(x) { capture.output(showMethods(x))[[1]] })
- funcSparkROrEmpty <- grepl("\\(package SparkR\\)$|^$", func)
- maskedBySparkR <- masked[funcSparkROrEmpty]
+ # This list should not change!
--- End diff --
just want to make sure people are aware that this list of names shouldn't be added to without considering what it means? if there's a better way to convey that let me know?
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/13636
Merged build finished. Test PASSed.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60471 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60471/consoleFull)** for PR 13636 at commit [`3f053ee`](https://github.com/apache/spark/commit/3f053eeee397d4d0b95267952e55cef9382d666a).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/13636
changed test output to show a diff, for example:
```
Failed -------------------------------------------------------------------------
1. Failure: Check masked functions (@test_context.R#35) ------------------------
length(maskedBySparkR) not equal to length(namesOfMasked).
1/1 mismatches
[1] 22 - 21 == 1
2. Failure: Check masked functions (@test_context.R#40) ------------------------
sort(maskedBySparkR, na.last = TRUE) not equal to sort(namesOfMasked, na.last = TRUE).
10/22 mismatches
x[13]: "rank"
y[13]: "rbind"
x[14]: "rbind"
y[14]: "sample"
x[15]: "sample"
y[15]: "sd"
x[16]: "sd"
y[16]: "startsWith"
x[17]: "startsWith"
y[17]: "subset"
x[18]: "rank"
y[18]: "rbind"
x[19]: "rbind"
y[19]: "sample"
x[20]: "sample"
y[20]: "sd"
x[21]: "sd"
y[21]: "startsWith"
x[22]: "startsWith"
y[22]: "subset"
```
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[GitHub] spark pull request #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R versi...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/13636#discussion_r67009490
--- Diff: R/pkg/inst/tests/testthat/test_context.R ---
@@ -19,21 +19,25 @@ context("test functions in sparkR.R")
test_that("Check masked functions", {
# Check that we are not masking any new function from base, stats, testthat unexpectedly
- masked <- conflicts(detail = TRUE)$`package:SparkR`
- expect_true("describe" %in% masked) # only when with testthat..
- func <- lapply(masked, function(x) { capture.output(showMethods(x))[[1]] })
- funcSparkROrEmpty <- grepl("\\(package SparkR\\)$|^$", func)
- maskedBySparkR <- masked[funcSparkROrEmpty]
+ # This list should not change!
--- End diff --
I'm not sure I follow what this comment means
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13636
LGTM. Thanks all. I will merge this after Jenkins passes
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60386 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60386/consoleFull)** for PR 13636 at commit [`a5eb3da`](https://github.com/apache/spark/commit/a5eb3daeb1d34e082e22176fd272dbe49398aaa8).
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[GitHub] spark pull request #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked f...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/13636#discussion_r67025422
--- Diff: R/pkg/inst/tests/testthat/test_context.R ---
@@ -19,21 +19,25 @@ context("test functions in sparkR.R")
test_that("Check masked functions", {
# Check that we are not masking any new function from base, stats, testthat unexpectedly
- masked <- conflicts(detail = TRUE)$`package:SparkR`
- expect_true("describe" %in% masked) # only when with testthat..
- func <- lapply(masked, function(x) { capture.output(showMethods(x))[[1]] })
- funcSparkROrEmpty <- grepl("\\(package SparkR\\)$|^$", func)
- maskedBySparkR <- masked[funcSparkROrEmpty]
+ # This list should not change!
--- End diff --
Yeah thats a good message to have. We can frame it as something like
```
NOTE: We should avoid adding entries to this list as masked functions make it hard for users to use base R functions.
```
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/13636
Thanks for testing. Updated as per the last comment.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60576 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60576/consoleFull)** for PR 13636 at commit [`014a5b6`](https://github.com/apache/spark/commit/014a5b67f10b484006bbe886c03d7525623278db).
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/13636
FYI, this is what I see running on R 3.3:
```
1. Error: string operators (@test_sparkSQL.R#1163) -----------------------------
unable to find an inherited method for function ‘startsWith’ for signature ‘"character"’
1: expect_true(startsWith("Hello World", "Hello")) at /opt/spark-2.0.0-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_sparkSQL.R:1163
2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
3: as.expectation(exp, ..., srcref = srcref)
4: identical(as.vector(object), TRUE)
5: as.vector(object)
6: startsWith("Hello World", "Hello")
7: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("character"), structure(function (x, prefix)
{
standardGeneric("startsWith")
}, generic = structure("startsWith", package = "SparkR"), package = "SparkR", group = list(), valueClass = character(0), signature = c("x",
"prefix"), default = `\001NULL\001`, skeleton = (function (x, prefix)
stop("invalid call in method dispatch to 'startsWith' (no default method)", domain = NA))(x,
prefix), class = structure("nonstandardGenericFunction", package = "methods")),
<environment>)
8: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
```
I will double check if there is indeed a problem with `startsWith("Hello World", "Hello")` when SparkR is loaded, or the tests are not up-to-date on what's being masked.
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[GitHub] spark pull request #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked f...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/13636
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the issue:
https://github.com/apache/spark/pull/13636
I'm still seeing errors after this change in my environment:
```
Failed -------------------------------------------------------------------------
1. Failure: Check masked functions (@test_context.R#31) ------------------------
length(maskedBySparkR) not equal to length(namesOfMasked).
1/1 mismatches
[1] 22 - 20 == 2
2. Failure: Check masked functions (@test_context.R#32) ------------------------
sort(maskedBySparkR) not equal to sort(namesOfMasked).
Lengths differ: 22 vs 20
DONE ===========================================================================
```
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[GitHub] spark pull request #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked f...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/13636#discussion_r67027738
--- Diff: R/pkg/inst/tests/testthat/test_context.R ---
@@ -19,21 +19,25 @@ context("test functions in sparkR.R")
test_that("Check masked functions", {
# Check that we are not masking any new function from base, stats, testthat unexpectedly
- masked <- conflicts(detail = TRUE)$`package:SparkR`
- expect_true("describe" %in% masked) # only when with testthat..
- func <- lapply(masked, function(x) { capture.output(showMethods(x))[[1]] })
- funcSparkROrEmpty <- grepl("\\(package SparkR\\)$|^$", func)
- maskedBySparkR <- masked[funcSparkROrEmpty]
+ # This list should not change!
--- End diff --
👍 right, and contact you? :)
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/13636
verified test passed and `startsWith` working
```
Welcome to
____ __
/ __/__ ___ _____/ /__
_\ \/ _ \/ _ `/ __/ '_/
/___/ .__/\_,_/_/ /_/\_\ version 2.0.0-SNAPSHOT
/_/
Spark context is available as sc, SQL context is available as sqlContext
> startsWith("Hello me", "Hello")
[1] TRUE
```
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the issue:
https://github.com/apache/spark/pull/13636
This passes tests for me on R 3.3.0 on OS X.
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the issue:
https://github.com/apache/spark/pull/13636
For reference, I was using
```
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
```
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/13636
Merged build finished. Test PASSed.
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13636
@liancheng we can use this PR to also address https://issues.apache.org/jira/browse/SPARK-15931
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/13636
Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/60477/
Test PASSed.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/13636
Merged build finished. Test PASSed.
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by liancheng <gi...@git.apache.org>.
Github user liancheng commented on the issue:
https://github.com/apache/spark/pull/13636
@shivaram True.
@felixcheung Could you please also add SPARK-15931 to the PR title if this PR also targets that one? Thanks.
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/13636
great point - @wangmiao1981 it looks like `startsWith` and `endsWith` are still masked on R 3.3?
re: PR #13476
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13636
LGTM. Just to confirm your local tests pass with R version > 3.2 ?
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60477 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60477/consoleFull)** for PR 13636 at commit [`92785ad`](https://github.com/apache/spark/commit/92785adac6c25a975a5fd41057ca21dd0225d3c9).
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60471 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60471/consoleFull)** for PR 13636 at commit [`3f053ee`](https://github.com/apache/spark/commit/3f053eeee397d4d0b95267952e55cef9382d666a).
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/13636
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by liancheng <gi...@git.apache.org>.
Github user liancheng commented on the issue:
https://github.com/apache/spark/pull/13636
Works for me too, passes tests on R 3.3.0 on OS X 10.10. Thanks!
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60477 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60477/consoleFull)** for PR 13636 at commit [`92785ad`](https://github.com/apache/spark/commit/92785adac6c25a975a5fd41057ca21dd0225d3c9).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #13636: [SPARK-15637][SPARKR] Remove R version check since maske...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/13636
Merged build finished. Test PASSed.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13636
Thanks @felixcheung - @JoshRosen / @liancheng can you also test this PR with R 3.3.0 before we merge ?
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/13636
**[Test build #60576 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/60576/consoleFull)** for PR 13636 at commit [`014a5b6`](https://github.com/apache/spark/commit/014a5b67f10b484006bbe886c03d7525623278db).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Remove R version chec...
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[GitHub] spark issue #13636: [SPARK-15637][SPARK-15931][SPARKR] Fix R masked function...
Posted by dongjoon-hyun <gi...@git.apache.org>.
Github user dongjoon-hyun commented on the issue:
https://github.com/apache/spark/pull/13636
This passes for me, too. Thank you, @felixcheung .
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