Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14433#discussion_r77205301
--- Diff: core/src/main/scala/org/apache/spark/internal/Logging.scala ---
@@ -135,7 +136,12 @@ private[spark] trait Logging {
val replLevel
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14783
@sun-rui Any other comments ?
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14856
Thanks @keypointt for the PR and @junyangq @felixcheung for reviewing.
Merging this into master
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14783
Jenkins, retest this please
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14903
Merging this into master and branch-2.0
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14903
Jenkins, retest this please
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14783
Sorry I think this was a break that I just fixed in #14904
Jenkins, retest this please.
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14904
Thanks - merging this to master, branch-2.0
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14904
cc @junyangq @felixcheung
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14903
The fix is in #14904
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GitHub user shivaram opened a pull request:
https://github.com/apache/spark/pull/14904
[SPARKR][SPARK-16581] Fix JVM API tests in SparkR
## What changes were proposed in this pull request?
Remove cleanup.jobj test. Use JVM wrapper API for other test cases.
## How
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14903
@junyangq @felixcheung The test error is due to an unrelated issue caused
when we upgraded testthat on Jenkins. I'm sending a fix for it now
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14784#discussion_r77073459
--- Diff: R/pkg/R/sparkR.R ---
@@ -365,6 +365,10 @@ sparkR.session <- function(
}
overrideEnvs(sparkConfigMap, param
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14889
Yeah lets open a separate JIRA to update testthat on the Jenkins boxes.
LGTM. Merging this to master and branch-2.0
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14784#discussion_r77031075
--- Diff: R/pkg/R/sparkR.R ---
@@ -365,6 +365,10 @@ sparkR.session <- function(
}
overrideEnvs(sparkConfigMap, param
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14859
Thanks @HyukjinKwon - Some comments:
- I think we can filter commits by `[SPARKR]` in the PR title. Changes to
core/ or sql/ could of course break the SparkR tests but it'll give us some
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14889
I just ran this on one of the Jenkins machines
```
> packageVersion("testthat")
[1] â0.11.0â
```
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14890
LGTM. Thanks @HyukjinKwon - Merging this to master
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14889
Thanks @HyukjinKwon - This is a great catch. LGTM pending tests.
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14744
Jenkins, retest this please
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14859
Good point on only running this on the master branch. We could even run it
periodically (say nightly) instead of on every commit.
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14775
Thanks @felixcheung - Addressed both the comments. Let me know if this
looks good.
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76654300
--- Diff: R/pkg/R/backend.R ---
@@ -25,9 +25,23 @@ isInstanceOf <- function(jobj, className) {
callJMethod(cls, "isInstanc
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76654243
--- Diff: R/pkg/R/backend.R ---
@@ -37,12 +51,42 @@ callJMethod <- function(objId, methodName, ...) {
invokeJava(isStatic = FALSE, objId
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76645788
--- Diff: R/pkg/DESCRIPTION ---
@@ -11,7 +11,7 @@ Authors@R: c(person("Shivaram", "Venkataraman", role =
c("aut", "cr
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14859
Thanks @HyukjinKwon - I for one would at least like the SparkR client to
work on Windows as I think there are quite a few R users who are on Windows.
@HyukjinKwon Could you add some
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76526127
--- Diff: R/pkg/DESCRIPTION ---
@@ -11,7 +11,7 @@ Authors@R: c(person("Shivaram", "Venkataraman", role =
c("aut", "cr
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14775
@felixcheung Good point about having a wrapper -- That will make it easier
to update the methods going forward. I added a new file `jvm.R` with the
wrapper functions.
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76523010
--- Diff: R/pkg/R/jobj.R ---
@@ -82,7 +82,20 @@ getClassName.jobj <- function(x) {
callJMethod(cls, "getName")
}
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522998
--- Diff: R/pkg/inst/tests/testthat/test_jvm_api.R ---
@@ -0,0 +1,41 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522995
--- Diff: R/pkg/R/jobj.R ---
@@ -82,7 +82,20 @@ getClassName.jobj <- function(x) {
callJMethod(cls, "getName")
}
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522987
--- Diff: R/pkg/R/jobj.R ---
@@ -82,7 +82,20 @@ getClassName.jobj <- function(x) {
callJMethod(cls, "getName")
}
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522986
--- Diff: R/pkg/R/backend.R ---
@@ -37,12 +51,42 @@ callJMethod <- function(objId, methodName, ...) {
invokeJava(isStatic = FALSE, objId
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522977
--- Diff: R/pkg/R/backend.R ---
@@ -37,12 +51,42 @@ callJMethod <- function(objId, methodName, ...) {
invokeJava(isStatic = FALSE, objId
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522953
--- Diff: R/pkg/R/backend.R ---
@@ -37,12 +51,42 @@ callJMethod <- function(objId, methodName, ...) {
invokeJava(isStatic = FALSE, objId
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522957
--- Diff: R/pkg/R/backend.R ---
@@ -37,12 +51,42 @@ callJMethod <- function(objId, methodName, ...) {
invokeJava(isStatic = FALSE, objId
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522952
--- Diff: R/pkg/R/backend.R ---
@@ -25,9 +25,23 @@ isInstanceOf <- function(jobj, className) {
callJMethod(cls, "isInstanc
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522940
--- Diff: R/pkg/R/backend.R ---
@@ -25,9 +25,23 @@ isInstanceOf <- function(jobj, className) {
callJMethod(cls, "isInstanc
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76522943
--- Diff: R/pkg/R/backend.R ---
@@ -25,9 +25,23 @@ isInstanceOf <- function(jobj, className) {
callJMethod(cls, "isInstanc
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14775#discussion_r76444282
--- Diff: R/pkg/NAMESPACE ---
@@ -363,4 +363,9 @@ S3method(structField, jobj)
S3method(structType, jobj)
S3method(structType, structField
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13584
Yeah I was going to say that we need to handle cases where `labels_output`
is also used. We can just add a numeric suffix maybe ?
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14774
LGTM. Thanks @wangmiao1981
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13584
Hmm - the problem still seems to be relevant. @mengxr @junyangq Would one
of you be able to look at this ?
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13584
@keypointt Is this PR still relevant ?
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14046
@sun-rui Is this PR still active ? Can we close it if its not relevant ?
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14744
LGTM. I agree that using SparkConf is preferable over environment variables
-- but it would be good to make the documentation clear on when each option is
used.
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14744#discussion_r76083596
--- Diff: docs/configuration.md ---
@@ -1752,6 +1752,13 @@ showDF(properties, numRows = 200, truncate = FALSE)
Executable for executing R scripts
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14783
Jenkins, ok to test
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14783
Thanks @clarkfitzg -- I'll take a look at this tomorrow
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14775
cc @felixcheung @olarayej
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GitHub user shivaram opened a pull request:
https://github.com/apache/spark/pull/14775
[SPARK-16581][SPARKR] Make JVM backend calling functions public
## What changes were proposed in this pull request?
This change exposes a public API in SparkR to create objects, call
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14741
The value of `what` shouldn't change if we are retrying the read. If it was
`integer` it should remain `integer`. There is a corner case of what happens if
we say read the first byte
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14447
@keypointt The error is happening because of the `href` line in the
`spark.mlp` documentation. If you move the opening brace to the previous line
the error goes away. i.e. the code should look
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14759
Merging this to master, branch-2.0
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14758
Hmm thats a good catch. Unfortunately it looks like CRAN only wants one
person / one email address to be in the Maintainer field. This is also
documented at http://r-pkgs.had.co.nz
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14759#discussion_r75781286
--- Diff: R/run-tests.sh ---
@@ -26,14 +26,35 @@ rm -f $LOGFILE
SPARK_TESTING=1 $FWDIR/../bin/spark-submit --driver-java-options
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14734
It was mostly manual -- I ran `dev/merge_spark_pr` and it prompted me to
say the cherry-pick has conflicts. I then opened another terminal and found
that the conflicts were in 3 files. I manually
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14734
I just did the merge in
https://github.com/apache/spark/commit/b65b041af8b64413c7d460d4ea110b2044d6f36e
-- Will be great if you can run CRAN checks using this and make sure I didn't
miss anything
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14759#discussion_r75776464
--- Diff: R/run-tests.sh ---
@@ -26,14 +26,35 @@ rm -f $LOGFILE
SPARK_TESTING=1 $FWDIR/../bin/spark-submit --driver-java-options
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14734
Hmm - let me give it a shot. If not I will open a fresh PR for `branch-2.0`
after doing a manual edit per file
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14759
So running `R/check-cran.sh` out of the box on master branch will fail.
However if you run `NO_TESTS=1 R/check-cran.sh` it should pass. Basically we
can't use check-cran.sh to run unit tests
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14734#discussion_r75772452
--- Diff: R/pkg/NAMESPACE ---
@@ -1,5 +1,9 @@
# Imports from base R
-importFrom(methods, setGeneric, setMethod, setOldClass)
+# Do not include
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14759
The new check I added doesn't run unit tests using `R CMD check`-- it only
checks the documentation etc. and thus works on the master branch as well.
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14759
@junyangq I guess we could - but it should be pretty simple to figure out
what is the problem given the entire log file ? FWIW the error we have right
now will be fixed when we merge #14734
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14759#discussion_r75766425
--- Diff: R/run-tests.sh ---
@@ -26,14 +26,30 @@ rm -f $LOGFILE
SPARK_TESTING=1 $FWDIR/../bin/spark-submit --driver-java-options
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14759#discussion_r75758514
--- Diff: R/run-tests.sh ---
@@ -26,14 +26,30 @@ rm -f $LOGFILE
SPARK_TESTING=1 $FWDIR/../bin/spark-submit --driver-java-options
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14759#discussion_r75758122
--- Diff: R/run-tests.sh ---
@@ -26,14 +26,30 @@ rm -f $LOGFILE
SPARK_TESTING=1 $FWDIR/../bin/spark-submit --driver-java-options
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14758
Merging to master, branch-2.0
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14759
cc @felixcheung @junyangq
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GitHub user shivaram opened a pull request:
https://github.com/apache/spark/pull/14759
[SPARK-16577][SPARKR] Add CRAN documentation checks to run-tests.sh
## What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
## How
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 user shivaram commented on the issue:
https://github.com/apache/spark/pull/14758
cc @mengxr @felixcheung
FYI - This is mostly to ensure that we can have more maintainers who can
update the CRAN submissions. This shouldn't affect anything else on the
development side
GitHub user shivaram opened a pull request:
https://github.com/apache/spark/pull/14758
[SPARKR][MINOR] Add Xiangrui and Felix to maintainers
## What changes were proposed in this pull request?
This change adds Xiangrui Meng and Felix Cheung to the maintainers field
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 user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14734#discussion_r75720021
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3058,7 +3057,7 @@ setMethod("str",
#' @note drop since 2.0.0
setMethod("drop",
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14734
LGTM. I had a couple of minor comments inline.
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14734#discussion_r75718809
--- Diff: R/pkg/R/generics.R ---
@@ -1339,7 +1339,6 @@ setGeneric("spark.naiveBayes", function(data,
formula, ...) { standardGeneric("s
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14734#discussion_r75718694
--- Diff: R/pkg/R/generics.R ---
@@ -1339,7 +1339,6 @@ setGeneric("spark.naiveBayes", function(data,
formula, ...) { standardGeneric("s
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14734#discussion_r75718243
--- Diff: R/pkg/R/DataFrame.R ---
@@ -3058,7 +3057,7 @@ setMethod("str",
#' @note drop since 2.0.0
setMethod("drop",
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14734#discussion_r75717898
--- Diff: R/pkg/NAMESPACE ---
@@ -1,5 +1,9 @@
# Imports from base R
-importFrom(methods, setGeneric, setMethod, setOldClass)
+# Do not include
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14734
@junyangq Could you take one more look ? I will also do a pass now
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14743
BTW LGTM. Merging this PR into master, branch-2.0
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14743
Thanks @HyukjinKwon -- this is a bit surprising as it was only recently
that you fixed the windows tests in
https://github.com/apache/spark/commit/1c403733b89258e57daf7b8b0a2011981ad7ed8a
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14743
@HyukjinKwon can you test this on Windows ?
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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
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
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 user shivaram commented on the issue:
https://github.com/apache/spark/pull/14489
The warning I got in `branch-2.0` before this PR was
```
Duplicated \argument entries in documentation object 'coltypes':
âxâ
```
With the backport this warning goes away
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
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
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14489
@felixcheung FYI I'm also backporting this to branch-2.0 as it gets rid of
one of the CRAN warnings.
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14639#discussion_r75344423
--- Diff: R/pkg/R/sparkR.R ---
@@ -344,6 +344,7 @@ sparkRHive.init <- function(jsc = NULL) {
#' @note sparkR.session since 2.0.0
sparkR.sess
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14639
@zjffdu Thanks for clarifying -- I now remember that in the YARN cluster
mode there is no `SPARK_HOME` set. However in this case the JVM comes up first
and the R process then connects to it. So
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14626
LGTM. Thanks @felixcheung - Merging this to master and branch-2.0
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14641
Thanks - Merging this to master
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14626#discussion_r74866185
--- Diff: R/pkg/R/generics.R ---
@@ -152,9 +146,9 @@ setGeneric("getNumPartitions", function(x) {
standardGeneric("getNumPartitions&q
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14182
This looks fine to me - @felixcheung feel free to merge this when you think
its good to go
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14522
Yeah LGTM. Merging this to master, branch-2.0 -- Thanks @junyangq
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Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/14626
I had one minor question about partitionBy -- otherwise change LGTM. Thanks
@felixcheung
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/14626#discussion_r74803446
--- Diff: R/pkg/R/generics.R ---
@@ -152,9 +146,9 @@ setGeneric("getNumPartitions", function(x) {
standardGeneric("getNumPartitions&q
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