Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126750717
Ah I see - so this affects things like the YARN cluster mode where the
spark-submit script and the driver are run on different machines ? How does
this work out
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7584#issuecomment-126746061
LGTM. Merging this
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7742#issuecomment-126517480
Merging this
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126531818
Thanks @brkyvz for the update. I had some minor style comments but I don't
quite follow why we had to move the initialization to SparkContext vs. having
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7764#issuecomment-126522020
Jenkins, retest this please
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7139#discussion_r35937520
--- Diff: core/src/main/scala/org/apache/spark/api/r/RBackend.scala ---
@@ -28,6 +28,7 @@ import io.netty.channel.socket.SocketChannel
import
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7764#issuecomment-126524783
@falaki the documentation builds are failing with an error message
```
Error :
/home/jenkins/workspace/SparkPullRequestBuilder@2/R/pkg/man/nrow.Rd
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7139#discussion_r35937603
--- Diff: core/src/main/scala/org/apache/spark/api/r/RUtils.scala ---
@@ -62,4 +64,7 @@ private[spark] object RUtils
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126765707
I see - so the right thing to do is to not build the package on every node
which needs this (driver / executor) but to build it once in the spark-submit
node
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126774354
Well we are unzipping the *source*, building a *binary* and then zipping
the *binary*. so its not redundant work :). The script right now only zips the
`lib/SparkR
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126778965
I think we can have multiple R packages in one zip. If I remember correctly
we just unzip the files in every executor (or spark-submit does this) and we
include
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126801147
Yep that sounds good to me. BTW the way R finds packages is using the
`.libPaths` contents. We explicitly set that to include `lib/` which is why it
can find `SparkR
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7764#discussion_r36016434
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1231,6 +1305,22 @@ setMethod(unionAll,
dataFrame(unioned)
})
+#' @title Union
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7764#issuecomment-126812352
Thanks @falaki for the update. LGTM. I had a minor style fix that I'll
apply during the merge.
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126815610
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-126815591
@brkyvz I'll take another pass later today and try this on YARN etc. We
should then be able to get it merged hopefully sometime this weekend.
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7701#issuecomment-125565050
Jenkins, ok to test
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7701#issuecomment-125565367
Thanks @trestletech -- Could you also add a small unit tests for this in
https://github.com/apache/spark/blob/15724fac569258d2a149507d8c767d0de0ae8306/R/pkg/inst/tests
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7701#issuecomment-125689494
LGTM. Thanks @trestletech -- Merging this
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7951#issuecomment-127845415
LGTM
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127811415
BTW @brkyvz can you merge the R changes in the
https://github.com/databricks/sbt-spark-package as well ?
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127810784
Yep - I'm out now, but will get back to my computer and merge
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7883#issuecomment-127134483
I don't think we need to do it on every run. If we need a new version of
lintr on Jenkins, then we can ask @JoshRosen or @shaneknapp to install a new
version
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7883#issuecomment-127132591
Also @yu-iskw I am not sure I understand why we need to install `lintr` in
the same library location as SparkR. That will mean that lintr will be
installed on every
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127132992
@brkyvz I just tried this out on a YARN cluster and I actually ran into an
error trying to use the CSV reader package. The command I ran was
```
./bin/sparkR
GitHub user shivaram opened a pull request:
https://github.com/apache/spark/pull/7899
[SPARK-9562] Change reference to amplab/spark-ec2 from mesos/
cc @srowen @pwendell @nchammas
You can merge this pull request into a Git repository by running:
$ git pull https://github.com
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127350331
I'm on it now. BTW is `sparkGLM` the best external package to try out in
YARN ? or is there a smaller demo package that I can use ?
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127390781
@brkyvz I tried to run this with YARN and found that the code to create the
`zip` might have some problems. It ends up creating a zip file which is
multiple gigabytes
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7764#discussion_r35903215
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1231,6 +1296,24 @@ setMethod(unionAll,
dataFrame(unioned)
})
+setGeneric
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7584#discussion_r35895264
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1384,7 +1384,7 @@ setMethod(saveAsTable,
org.apache.spark.sql.parquet
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7795#issuecomment-126401982
Thanks @yu-iskw -- LGTM. Merging this
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7742#issuecomment-126517276
LGTM
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7139#discussion_r35937631
--- Diff:
yarn/src/test/scala/org/apache/spark/deploy/yarn/YarnClusterSuite.scala ---
@@ -22,6 +22,9 @@ import java.net.URL
import java.util.Properties
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7764#discussion_r35896170
--- Diff: R/pkg/R/DataFrame.R ---
@@ -534,6 +552,53 @@ setMethod(count,
callJMethod(x@sdf, count)
})
+#' @rdname
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7764#discussion_r35897285
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1231,6 +1296,24 @@ setMethod(unionAll,
dataFrame(unioned)
})
+setGeneric
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7742#discussion_r35897965
--- Diff: core/src/main/scala/org/apache/spark/api/r/RBackendHandler.scala
---
@@ -148,6 +151,9 @@ private[r] class RBackendHandler(server: RBackend
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7764#discussion_r35896690
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1231,6 +1296,24 @@ setMethod(unionAll,
dataFrame(unioned)
})
+setGeneric
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7750#issuecomment-126414664
LGTM. Merging this
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7647#issuecomment-126415405
Not sure I get it -- Does this mean the increased size will only work if we
use the `resizefs` in a script ?
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-128844893
Jenkins, retest this please
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/8085#discussion_r36782862
--- Diff: docs/sparkr.md ---
@@ -210,6 +210,43 @@ head(df)
{% endhighlight %}
/div
+### Model Formulae
+
+SparkR allows
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/8085#discussion_r36782153
--- Diff: docs/sparkr.md ---
@@ -210,6 +210,43 @@ head(df)
{% endhighlight %}
/div
+### Model Formulae
--- End diff --
+1. I
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8085#issuecomment-130012889
Thanks @ericl - I just left some inline comments.
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/8085#discussion_r36782425
--- Diff: docs/sparkr.md ---
@@ -210,6 +210,43 @@ head(df)
{% endhighlight %}
/div
+### Model Formulae
+
--- End diff
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7139#discussion_r36211625
--- Diff: core/src/main/scala/org/apache/spark/api/r/RUtils.scala ---
@@ -19,6 +19,8 @@ package org.apache.spark.api.r
import java.io.File
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7494#issuecomment-127663833
I see - so the problem here is on how to write a unit test that uses UTF-8
and works with `LC_ALL=C` ? One simple thing we might be able to do is to set
the locale
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127664838
@brkyvz I think I figured out the problem with Jenkins -- Since Jenkins
uses SBT it doesn't build the SparkR package at the beginning along with the
rest
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127677811
Thanks @brkyvz -- Changes LGTM. Can you check if @andrewor14 wants to take
another look at the SparkSubmit changes ?
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/6599#issuecomment-128448874
@JoshRosen @zsxwing Any thoughts on merging this for 1.5 ?
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7494#issuecomment-128447851
Can we still use the `iconv` solution with the `System.setlocale` in the
test case ? It doesn't seem right to use `rawToChar` when we are decoding UTF-8
strings
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7139#issuecomment-127740630
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-128744494
LGTM. Thanks @vanzin for the fix. cc @brkyvz
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-128744287
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-128787880
Sigh -- our tests are too flaky.
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8162#issuecomment-130769302
Is there any major reason for doing this ? I've still seen some clusters /
workloads (as of Spark 1.3) where nio works better than netty and I didn't get
a chance
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8162#issuecomment-130978310
Yeah I'll try to produce a small test case for this next time I run into
this.
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7461#issuecomment-129506547
Thanks @kmadhugit , the test case sounds good to me. Could you try this on
a multi-node cluster ? We just set the locality preference for the scheduler
and I guess
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129223162
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8055#issuecomment-129226373
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7494#issuecomment-129227462
@CHOIJAEHONG1 This diff is looking good. Can you update the PR with this ?
BTW why do we need to clear the encoding bit in `context.R` ? Does the
serialization
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129260689
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8055#issuecomment-129235074
@brkyvz Removed the test case now. I'm not sure adding a comment is really
relevant as the argument to the method is an `Option`. And you are right that
we can't quite
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129232005
@tdas @rxin I've see the test `SPARK-6222: Do not clear received block data
too soon` fail a bunch of times (on Jenkins and on local runs) - Example stack
trace at [1
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129528087
Yeah I was wondering the same thing. In fact I think the tests have managed
to pass piece-wise (i.e. core sometimes, streaming sometimes, sql sometimes
etc
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129506725
Jenkins, retest this please
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/8194#discussion_r37092050
--- Diff: R/pkg/R/functions.R ---
@@ -67,6 +67,14 @@ createFunctions - function() {
createFunctions()
+#' @rdname functions
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/8194#discussion_r37092120
--- Diff: R/pkg/R/generics.R ---
@@ -682,6 +682,10 @@ setGeneric(cbrt, function(x) {
standardGeneric(cbrt) })
#' @export
setGeneric(ceil, function
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8194#issuecomment-131165945
Thanks @yu-iskw. I left some comments inline. One more thing we need to do
is to update our `NAMESPACE` file [1] with all the functions we have added so
far
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/8194#discussion_r37092216
--- Diff: R/pkg/R/generics.R ---
@@ -794,6 +806,10 @@ setGeneric(size, function(x) {
standardGeneric(size) })
#' @export
setGeneric(soundex
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8220#issuecomment-131306428
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7419#issuecomment-131412001
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7419#issuecomment-131412095
Thanks @sun-rui -- this fix is simple and looks good. Couple of minor things
1. There is an empty file `nohup.out` added in the PR which needs to be
removed
2
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8220#issuecomment-131412272
LGTM. I think we should merge this into `branch-1.5` as well.
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8220#issuecomment-131412441
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8085#issuecomment-130124028
LGTM
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-128884477
Sigh, I guess today is not a good day to get tests passed.
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129013022
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7774#issuecomment-129021145
@zsxwing @rxin I just ran into a problem with the annotation thing that was
discussed earlier in this PR.
My master branch is clean and is at
https://github.com
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129058361
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7599#issuecomment-129059640
@brkyvz I ran into a trouble using `sparkR` with the CSV package from the
master branch and I think this PR might be the related to the problem. If I run
`./bin/sparkR
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129080680
@JoshRosen @rxin This PR has failed Jenkins 6 (!) times with unrelated
failures. Are there any known issues or flaky tests ? I'd like to get this fix
into 1.5
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7774#issuecomment-129081760
I just realized I missed pasting the first two lines of the error
```
error: error while loading SQLListener, Missing dependency 'bad symbolic
reference
GitHub user shivaram opened a pull request:
https://github.com/apache/spark/pull/8055
[CORE] [SPARK-9760] Use Option instead of Some for Ivy repos
This was introduced in #7599
cc @rxin @brkyvz
You can merge this pull request into a Git repository by running:
$ git
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8055#issuecomment-129088465
Also I am not sure how to add a test case for this as our existing unit
tests use a custom Ivy repository which is always specified in
`--repositories`. The bug only
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8055#issuecomment-129100227
Added a test case but I'm not sure how useful it is as a lot of things can
throw a RuntimeException ? @rxin let me know if its worth having it vs. a few
seconds added
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/8008#issuecomment-129103841
I give up. I'm going to manually patch this on a clean branch on my laptop
and run `dev/run-tests` and report back if it passes
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7912#discussion_r36206750
--- Diff: docs/README.md ---
@@ -8,6 +8,16 @@ Read on to learn more about viewing documentation in plain
text (i.e., markdown)
documentation yourself
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7883#issuecomment-128426622
Thanks @yu-iskw for the update. The code changes mostly look good to me.
Lets wait for @JoshRosen to take another look at this as there have been some
flaky builds
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7584#issuecomment-123773927
Jenkins, retest this please
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7584#issuecomment-123775036
I think most of the changes are fine. The `!` ones look a little awkward
and I want to check the `prev@func` issue to see why lint-r is complaining
about
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7584#issuecomment-123782306
@shaneknapp Can you manually delete the jar ? The script should
auto-download a good version then AFAIK
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Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7584#issuecomment-12319
@shaneknapp @JoshRosen Looks like there is a problem with Jenkins. The
builds seem to be failing with
```
Launching sbt from build/sbt-launch-0.13.7.jar
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7318#issuecomment-123818662
@mengxr I guess we will have a new PR for the documentation update, so this
PR LGTM. I will merge this unless you have anything else to add
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7584#discussion_r35237914
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1384,7 +1384,7 @@ setMethod(saveAsTable,
org.apache.spark.sql.parquet
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7596#issuecomment-123788290
I am not sure taking in the credentials in plain text is the best solution
-- Can we get this from some other environment variable and / or boto's config
files etc
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7584#discussion_r35237834
--- Diff: R/pkg/R/RDD.R ---
@@ -85,7 +85,7 @@ setMethod(initialize, PipelinedRDD, function(.Object,
prev, func, jrdd_val)
isPipelinable
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7584#discussion_r35437342
--- Diff: R/pkg/R/DataFrame.R ---
@@ -1384,7 +1384,7 @@ setMethod(saveAsTable,
org.apache.spark.sql.parquet
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7640#issuecomment-124569224
LGTM. I had one minor comment -- I'll fix this up during merge
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Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/7640#discussion_r35437569
--- Diff: R/pkg/R/sparkR.R ---
@@ -104,16 +104,14 @@ sparkR.init - function(
return(get(.sparkRjsc, envir = .sparkREnv
Github user shivaram commented on the pull request:
https://github.com/apache/spark/pull/7419#issuecomment-124569785
@sun-rui Any update on this ?
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