## What changes were proposed in this pull request?
This change exposes a public API in SparkR to create objects, call methods on the Spark driver JVM
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Unit tests, CRAN checks
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#14775 from shivaram/sparkr-java-api.
## What changes were proposed in this pull request?
This PR tries to fix the name of the `SparkDataFrame` used in the example. Also, it gives a reference url of an example data file so that users can play with.
## How was this patch tested?
Manual test.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14853 from junyangq/SPARKR-FixLDADoc.
## What changes were proposed in this pull request?
The original example doesn't work because the features are not categorical. This PR fixes this by changing to another dataset.
## How was this patch tested?
Manual test.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14820 from junyangq/SPARK-FixNaiveBayes.
## What changes were proposed in this pull request?
This PR gives informative message to users when they try to connect to a remote master but don't have Spark package in their local machine.
As a clarification, for now, automatic installation will only happen if they start SparkR in R console (rather than from sparkr-shell) and connect to local master. In the remote master mode, local Spark package is still needed, but we will not trigger the install.spark function because the versions have to match those on the cluster, which involves more user input. Instead, we here try to provide detailed message that may help the users.
Some of the other messages have also been slightly changed.
## How was this patch tested?
Manual test.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14761 from junyangq/SPARK-16579-V1.
## What changes were proposed in this pull request?
This PR adds more examples to window function docs to make them more accessible to the users.
It also fixes default value issues for `lag` and `lead`.
## How was this patch tested?
Manual test, R unit test.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14779 from junyangq/SPARKR-FixWindowFunctionDocs.
## What changes were proposed in this pull request?
Fixed several misplaced param tag - they should be on the spark.* method generics
## How was this patch tested?
run knitr
junyangq
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14792 from felixcheung/rdocmllib.
https://issues.apache.org/jira/browse/SPARK-16445
## What changes were proposed in this pull request?
Create Multilayer Perceptron Classifier wrapper in SparkR
## How was this patch tested?
Tested manually on local machine
Author: Xin Ren <iamshrek@126.com>
Closes#14447 from keypointt/SPARK-16445.
## What changes were proposed in this pull request?
The original doc of `show` put methods for multiple classes together but the text only talks about `SparkDataFrame`. This PR tries to fix this problem.
## How was this patch tested?
Manual test.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14776 from junyangq/SPARK-FixShowDoc.
## What changes were proposed in this pull request?
The PR removes reference link in the doc for environment variables for common Windows folders. The cran check gave code 503: service unavailable on the original link.
## How was this patch tested?
Manual check.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14767 from junyangq/SPARKR-RemoveLink.
## What changes were proposed in this pull request?
Update DESCRIPTION
## How was this patch tested?
Run install and CRAN tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14764 from felixcheung/rpackagedescription.
## What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
## How was this patch tested?
This change adds CRAN documentation checks to be run as a part of `R/run-tests.sh` . As this script is also used by Jenkins this means that we will get documentation checks on every PR going forward.
(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#14759 from shivaram/sparkr-cran-jenkins.
## What changes were proposed in this pull request?
replace ``` ` ``` in code doc with `\code{thing}`
remove added `...` for drop(DataFrame)
fix remaining CRAN check warnings
## How was this patch tested?
create doc with knitr
junyangq
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14734 from felixcheung/rdoccleanup.
## What changes were proposed in this pull request?
This change adds Xiangrui Meng and Felix Cheung to the maintainers field in the package description.
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#14758 from shivaram/sparkr-maintainers.
## What changes were proposed in this pull request?
refactor, cleanup, reformat, fix deprecation in test
## How was this patch tested?
unit tests, manual tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14735 from felixcheung/rmllibutil.
## What changes were proposed in this pull request?
This PR tries to fix the scheme of local cache folder in Windows. The name of the environment variable should be `LOCALAPPDATA` rather than `%LOCALAPPDATA%`.
## How was this patch tested?
Manual test in Windows 7.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14743 from junyangq/SPARKR-FixWindowsInstall.
## What changes were proposed in this pull request?
Ignore temp files generated by `check-cran.sh`.
Author: Xiangrui Meng <meng@databricks.com>
Closes#14740 from mengxr/R-gitignore.
## What changes were proposed in this pull request?
#14551 fixed off-by-one bug in ```randomizeInPlace``` and some test failure caused by this fix.
But for SparkR ```spark.gaussianMixture``` test case, the fix is inappropriate. It only changed the output result of native R which should be compared by SparkR, however, it did not change the R code in annotation which is used for reproducing the result in native R. It will confuse users who can not reproduce the same result in native R. This PR sends a more robust test case which can produce same result between SparkR and native R.
## How was this patch tested?
Unit test update.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#14730 from yanboliang/spark-16961-followup.
## What changes were proposed in this pull request?
This PR tries to fix all the remaining "undocumented/duplicated arguments" warnings given by CRAN-check.
One left is doc for R `stats::glm` exported in SparkR. To mute that warning, we have to also provide document for all arguments of that non-SparkR function.
Some previous conversation is in #14558.
## How was this patch tested?
R unit test and `check-cran.sh` script (with no-test).
Author: Junyang Qian <junyangq@databricks.com>
Closes#14705 from junyangq/SPARK-16508-master.
JIRA issue link:
https://issues.apache.org/jira/browse/SPARK-16961
Changed one line of Utils.randomizeInPlace to allow elements to stay in place.
Created a unit test that runs a Pearson's chi squared test to determine whether the output diverges significantly from a uniform distribution.
Author: Nick Lavers <nick.lavers@videoamp.com>
Closes#14551 from nicklavers/SPARK-16961-randomizeInPlace.
## What changes were proposed in this pull request?
Add LDA Wrapper in SparkR with the following interfaces:
- spark.lda(data, ...)
- spark.posterior(object, newData, ...)
- spark.perplexity(object, ...)
- summary(object)
- write.ml(object)
- read.ml(path)
## How was this patch tested?
Test with SparkR unit test.
Author: Xusen Yin <yinxusen@gmail.com>
Closes#14229 from yinxusen/SPARK-16447.
## What changes were proposed in this pull request?
Gaussian Mixture Model wrapper in SparkR, similarly to R's ```mvnormalmixEM```.
## How was this patch tested?
Unit test.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#14392 from yanboliang/spark-16446.
## What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
Add Isotonic Regression wrapper in SparkR
Wrappers in R and Scala are added.
Unit tests
Documentation
## How was this patch tested?
Manually tested with sudo ./R/run-tests.sh
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#14182 from wangmiao1981/isoR.
## What changes were proposed in this pull request?
Rename RDD functions for now to avoid CRAN check warnings.
Some RDD functions are sharing generics with DataFrame functions (hence the problem) so after the renames we need to add new generics, for now.
## How was this patch tested?
unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14626 from felixcheung/rrddfunctions.
## What changes were proposed in this pull request?
Fix the issue that ```spark.glm``` ```weightCol``` should in the signature.
## How was this patch tested?
Existing tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#14641 from yanboliang/weightCol.
## What changes were proposed in this pull request?
Add an install_spark function to the SparkR package. User can run `install_spark()` to install Spark to a local directory within R.
Updates:
Several changes have been made:
- `install.spark()`
- check existence of tar file in the cache folder, and download only if not found
- trial priority of mirror_url look-up: user-provided -> preferred mirror site from apache website -> hardcoded backup option
- use 2.0.0
- `sparkR.session()`
- can install spark when not found in `SPARK_HOME`
## How was this patch tested?
Manual tests, running the check-cran.sh script added in #14173.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14258 from junyangq/SPARK-16579.
## What changes were proposed in this pull request?
Training GLMs on weighted dataset is very important use cases, but it is not supported by SparkR currently. Users can pass argument ```weights``` to specify the weights vector in native R. For ```spark.glm```, we can pass in the ```weightCol``` which is consistent with MLlib.
## How was this patch tested?
Unit test.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#14346 from yanboliang/spark-16710.
## What changes were proposed in this pull request?
This change moves the include jar test from R to SparkSubmitSuite and uses a dynamically compiled jar. This helps us remove the binary jar from the R package and solves both the CRAN warnings and the lack of source being available for this jar.
## How was this patch tested?
SparkR unit tests, SparkSubmitSuite, check-cran.sh
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#14243 from shivaram/sparkr-jar-move.
## What changes were proposed in this pull request?
https://issues.apache.org/jira/browse/SPARK-16055
sparkPackages - argument is passed and we detect that we are in the R script mode, we should print some warning like --packages flag should be used with with spark-submit
## How was this patch tested?
In my system locally
Author: krishnakalyan3 <krishnakalyan3@gmail.com>
Closes#14179 from krishnakalyan3/spark-pkg.
## What changes were proposed in this pull request?
Fix R SparkSession init/stop, and warnings of reusing existing Spark Context
## How was this patch tested?
unit tests
shivaram
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14177 from felixcheung/rsessiontest.
## What changes were proposed in this pull request?
Add a check-cran.sh script that runs `R CMD check` as CRAN. Also fixes a number of issues pointed out by the check. These include
- Updating `DESCRIPTION` to be appropriate
- Adding a .Rbuildignore to ignore lintr, src-native, html that are non-standard files / dirs
- Adding aliases to all S4 methods in DataFrame, Column, GroupedData etc. This is required as stated in https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-S4-classes-and-methods
- Other minor fixes
## How was this patch tested?
SparkR unit tests, running the above mentioned script
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#14173 from shivaram/sparkr-cran-changes.
## What changes were proposed in this pull request?
More tests
I don't think this is critical for Spark 2.0.0 RC, maybe Spark 2.0.1 or 2.1.0.
## How was this patch tested?
unit tests
shivaram dongjoon-hyun
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14206 from felixcheung/rroutetests.
## What changes were proposed in this pull request?
Fix function routing to work with and without namespace operator `SparkR::createDataFrame`
## How was this patch tested?
manual, unit tests
shivaram
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14195 from felixcheung/rroutedefault.
## What changes were proposed in this pull request?
Rename window.partitionBy and window.orderBy to windowPartitionBy and windowOrderBy to pass CRAN package check.
## How was this patch tested?
SparkR unit tests.
Author: Sun Rui <sunrui2016@gmail.com>
Closes#14192 from sun-rui/SPARK-16509.
## What changes were proposed in this pull request?
Minor documentation update for code example, code style, and missed reference to "sparkR.init"
## How was this patch tested?
manual
shivaram
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14178 from felixcheung/rcsvprogrammingguide.
## What changes were proposed in this pull request?
Minor example updates
## How was this patch tested?
manual
shivaram
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14171 from felixcheung/rexample.
## What changes were proposed in this pull request?
* Update SparkR ML section to make them consistent with SparkR API docs.
* Since #13972 adds labelling support for the ```include_example``` Jekyll plugin, so that we can split the single ```ml.R``` example file into multiple line blocks with different labels, and include them in different algorithms/models in the generated HTML page.
## How was this patch tested?
Only docs update, manually check the generated docs.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#14011 from yanboliang/r-user-guide-update.
## What changes were proposed in this pull request?
This PR prevents ERRORs when `summary(df)` is called for `SparkDataFrame` with not-numeric columns. This failure happens only in `SparkR`.
**Before**
```r
> df <- createDataFrame(faithful)
> df <- withColumn(df, "boolean", df$waiting==79)
> summary(df)
16/07/07 14:15:16 ERROR RBackendHandler: describe on 34 failed
Error in invokeJava(isStatic = FALSE, objId$id, methodName, ...) :
org.apache.spark.sql.AnalysisException: cannot resolve 'avg(`boolean`)' due to data type mismatch: function average requires numeric types, not BooleanType;
```
**After**
```r
> df <- createDataFrame(faithful)
> df <- withColumn(df, "boolean", df$waiting==79)
> summary(df)
SparkDataFrame[summary:string, eruptions:string, waiting:string]
```
## How was this patch tested?
Pass the Jenkins with a updated testcase.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#14096 from dongjoon-hyun/SPARK-16425.
## What changes were proposed in this pull request?
Apply default "NA" as null string for R, like R read.csv na.string parameter.
https://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html
na.strings = "NA"
An user passing a csv file with NA value should get the same behavior with SparkR read.df(... source = "csv")
(couldn't open JIRA, will do that later)
## How was this patch tested?
unit tests
shivaram
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13984 from felixcheung/rcsvnastring.
## What changes were proposed in this pull request?
ORC test should be enabled only when HiveContext is available.
## How was this patch tested?
Manual.
```
$ R/run-tests.sh
...
1. create DataFrame from RDD (test_sparkSQL.R#200) - Hive is not build with SparkSQL, skipped
2. test HiveContext (test_sparkSQL.R#1021) - Hive is not build with SparkSQL, skipped
3. read/write ORC files (test_sparkSQL.R#1728) - Hive is not build with SparkSQL, skipped
4. enableHiveSupport on SparkSession (test_sparkSQL.R#2448) - Hive is not build with SparkSQL, skipped
5. sparkJars tag in SparkContext (test_Windows.R#21) - This test is only for Windows, skipped
DONE ===========================================================================
Tests passed.
```
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#14019 from dongjoon-hyun/SPARK-16233.
## What changes were proposed in this pull request?
Capture errors from R workers in daemon.R to avoid deletion of R session temporary directory. See detailed description at https://issues.apache.org/jira/browse/SPARK-16299
## How was this patch tested?
SparkR unit tests.
Author: Sun Rui <sunrui2016@gmail.com>
Closes#13975 from sun-rui/SPARK-16299.
## What changes were proposed in this pull request?
gapplyCollect() does gapply() on a SparkDataFrame and collect the result back to R. Compared to gapply() + collect(), gapplyCollect() offers performance optimization as well as programming convenience, as no schema is needed to be provided.
This is similar to dapplyCollect().
## How was this patch tested?
Added test cases for gapplyCollect similar to dapplyCollect
Author: Narine Kokhlikyan <narine@slice.com>
Closes#13760 from NarineK/gapplyCollect.
## What changes were proposed in this pull request?
This PR implements `posexplode` table generating function. Currently, master branch raises the following exception for `map` argument. It's different from Hive.
**Before**
```scala
scala> sql("select posexplode(map('a', 1, 'b', 2))").show
org.apache.spark.sql.AnalysisException: No handler for Hive UDF ... posexplode() takes an array as a parameter; line 1 pos 7
```
**After**
```scala
scala> sql("select posexplode(map('a', 1, 'b', 2))").show
+---+---+-----+
|pos|key|value|
+---+---+-----+
| 0| a| 1|
| 1| b| 2|
+---+---+-----+
```
For `array` argument, `after` is the same with `before`.
```
scala> sql("select posexplode(array(1, 2, 3))").show
+---+---+
|pos|col|
+---+---+
| 0| 1|
| 1| 2|
| 2| 3|
+---+---+
```
## How was this patch tested?
Pass the Jenkins tests with newly added testcases.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13971 from dongjoon-hyun/SPARK-16289.
https://issues.apache.org/jira/browse/SPARK-16140
## What changes were proposed in this pull request?
Group the R doc of spark.kmeans, predict(KM), summary(KM), read/write.ml(KM) under Rd spark.kmeans. The example code was updated.
## How was this patch tested?
Tested on my local machine
And on my laptop `jekyll build` is failing to build API docs, so here I can only show you the html I manually generated from Rd files, with no CSS applied, but the doc content should be there.
Author: Xin Ren <iamshrek@126.com>
Closes#13921 from keypointt/SPARK-16140.
