## What changes were proposed in this pull request?
Add wrappers for `o.a.s.sql.functions`:
- `split` as `split_string`
- `repeat` as `repeat_string`
## How was this patch tested?
Existing tests, additional unit tests, `check-cran.sh`
Author: zero323 <zero323@users.noreply.github.com>
Closes#17729 from zero323/SPARK-20438.
## What changes were proposed in this pull request?
Adds wrappers for `collect_list` and `collect_set`.
## How was this patch tested?
Unit tests, `check-cran.sh`
Author: zero323 <zero323@users.noreply.github.com>
Closes#17672 from zero323/SPARK-20371.
## What changes were proposed in this pull request?
Adds wrappers for `o.a.s.sql.functions.array` and `o.a.s.sql.functions.map`
## How was this patch tested?
Unit tests, `check-cran.sh`
Author: zero323 <zero323@users.noreply.github.com>
Closes#17674 from zero323/SPARK-20375.
## What changes were proposed in this pull request?
Following up on #17483, add createTable (which is new in 2.2.0) and deprecate createExternalTable, plus a number of minor fixes
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17511 from felixcheung/rceatetable.
## What changes were proposed in this pull request?
Adds SparkR API for FPGrowth: [SPARK-19825](https://issues.apache.org/jira/browse/SPARK-19825):
- `spark.fpGrowth` -model training.
- `freqItemsets` and `associationRules` methods with new corresponding generics.
- Scala helper: `org.apache.spark.ml.r. FPGrowthWrapper`
- unit tests.
## How was this patch tested?
Feature specific unit tests.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17170 from zero323/SPARK-19825.
## What changes were proposed in this pull request?
Add a set of catalog API in R
```
"currentDatabase",
"listColumns",
"listDatabases",
"listFunctions",
"listTables",
"recoverPartitions",
"refreshByPath",
"refreshTable",
"setCurrentDatabase",
```
https://github.com/apache/spark/pull/17483/files#diff-6929e6c5e59017ff954e110df20ed7ff
## How was this patch tested?
manual tests, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17483 from felixcheung/rcatalog.
## What changes were proposed in this pull request?
Add checkpoint, setCheckpointDir API to R
## How was this patch tested?
unit tests, manual tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17351 from felixcheung/rdfcheckpoint.
## What changes were proposed in this pull request?
Add "experimental" API for SS in R
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16982 from felixcheung/rss.
## What changes were proposed in this pull request?
Add column functions: to_json, from_json, and tests covering error cases.
## How was this patch tested?
unit tests, manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17134 from felixcheung/rtojson.
## What changes were proposed in this pull request?
Add coalesce on DataFrame for down partitioning without shuffle and coalesce on Column
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16739 from felixcheung/rcoalesce.
## What changes were proposed in this pull request?
Linear SVM classifier is newly added into ML and python API has been added. This JIRA is to add R side API.
Marked as WIP, as I am designing unit tests.
## How was this patch tested?
Please review http://spark.apache.org/contributing.html before opening a pull request.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16800 from wangmiao1981/svc.
## What changes were proposed in this pull request?
This pull request adds two new user facing functions:
- `to_date` which accepts an expression and a format and returns a date.
- `to_timestamp` which accepts an expression and a format and returns a timestamp.
For example, Given a date in format: `2016-21-05`. (YYYY-dd-MM)
### Date Function
*Previously*
```
to_date(unix_timestamp(lit("2016-21-05"), "yyyy-dd-MM").cast("timestamp"))
```
*Current*
```
to_date(lit("2016-21-05"), "yyyy-dd-MM")
```
### Timestamp Function
*Previously*
```
unix_timestamp(lit("2016-21-05"), "yyyy-dd-MM").cast("timestamp")
```
*Current*
```
to_timestamp(lit("2016-21-05"), "yyyy-dd-MM")
```
### Tasks
- [X] Add `to_date` to Scala Functions
- [x] Add `to_date` to Python Functions
- [x] Add `to_date` to SQL Functions
- [X] Add `to_timestamp` to Scala Functions
- [x] Add `to_timestamp` to Python Functions
- [x] Add `to_timestamp` to SQL Functions
- [x] Add function to R
## How was this patch tested?
- [x] Add Functions to `DateFunctionsSuite`
- Test new `ParseToTimestamp` Expression (*not necessary*)
- Test new `ParseToDate` Expression (*not necessary*)
- [x] Add test for R
- [x] Add test for Python in test.py
Please review http://spark.apache.org/contributing.html before opening a pull request.
Author: anabranch <wac.chambers@gmail.com>
Author: Bill Chambers <bill@databricks.com>
Author: anabranch <bill@databricks.com>
Closes#16138 from anabranch/SPARK-16609.
## What changes were proposed in this pull request?
add header
## How was this patch tested?
Manual run to check vignettes html is created properly
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16709 from felixcheung/rfilelicense.
## What changes were proposed in this pull request?
With doc to say this would convert DF into RDD
## How was this patch tested?
unit tests, manual tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16668 from felixcheung/rgetnumpartitions.
## What changes were proposed in this pull request?
Add R wrapper for bisecting Kmeans.
As JIRA is down, I will update title to link with corresponding JIRA later.
## How was this patch tested?
Add new unit tests.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16566 from wangmiao1981/bk.
## What changes were proposed in this pull request?
It would make it easier to integrate with other component expecting row-based JSON format.
This replaces the non-public toJSON RDD API.
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16368 from felixcheung/rJSON.
## What changes were proposed in this pull request?
API for SparkUI URL from SparkContext
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16367 from felixcheung/rwebui.
## What changes were proposed in this pull request?
This PR has 2 key changes. One, we are building source package (aka bundle package) for SparkR which could be released on CRAN. Two, we should include in the official Spark binary distributions SparkR installed from this source package instead (which would have help/vignettes rds needed for those to work when the SparkR package is loaded in R, whereas earlier approach with devtools does not)
But, because of various differences in how R performs different tasks, this PR is a fair bit more complicated. More details below.
This PR also includes a few minor fixes.
### more details
These are the additional steps in make-distribution; please see [here](https://github.com/apache/spark/blob/master/R/CRAN_RELEASE.md) on what's going to a CRAN release, which is now run during make-distribution.sh.
1. package needs to be installed because the first code block in vignettes is `library(SparkR)` without lib path
2. `R CMD build` will build vignettes (this process runs Spark/SparkR code and captures outputs into pdf documentation)
3. `R CMD check` on the source package will install package and build vignettes again (this time from source packaged) - this is a key step required to release R package on CRAN
(will skip tests here but tests will need to pass for CRAN release process to success - ideally, during release signoff we should install from the R source package and run tests)
4. `R CMD Install` on the source package (this is the only way to generate doc/vignettes rds files correctly, not in step # 1)
(the output of this step is what we package into Spark dist and sparkr.zip)
Alternatively,
R CMD build should already be installing the package in a temp directory though it might just be finding this location and set it to lib.loc parameter; another approach is perhaps we could try calling `R CMD INSTALL --build pkg` instead.
But in any case, despite installing the package multiple times this is relatively fast.
Building vignettes takes a while though.
## How was this patch tested?
Manually, CI.
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16014 from felixcheung/rdist.
## What changes were proposed in this pull request?
Gradient Boosted Tree in R.
With a few minor improvements to RandomForest in R.
Since this is relatively isolated I'd like to target this for branch-2.1
## How was this patch tested?
manual tests, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#15746 from felixcheung/rgbt.
## What changes were proposed in this pull request?
Random Forest Regression and Classification for R
Clean-up/reordering generics.R
## How was this patch tested?
manual tests, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#15607 from felixcheung/rrandomforest.
## What changes were proposed in this pull request?
As we discussed in #14818, I added a separate R wrapper spark.logit for logistic regression.
This single interface supports both binary and multinomial logistic regression. It also has "predict" and "summary" for binary logistic regression.
## How was this patch tested?
New unit tests are added.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#15365 from wangmiao1981/glm.
## What changes were proposed in this pull request?
Add storageLevel to DataFrame for SparkR.
This is similar to this RP: https://github.com/apache/spark/pull/13780
but in R I do not make a class for `StorageLevel`
but add a method `storageToString`
## How was this patch tested?
test added.
Author: WeichenXu <WeichenXu123@outlook.com>
Closes#15516 from WeichenXu123/storageLevel_df_r.
## What changes were proposed in this pull request?
Add crossJoin and do not default to cross join if joinExpr is left out
## How was this patch tested?
unit test
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#15559 from felixcheung/rcrossjoin.
## What changes were proposed in this pull request?
Fix for a bunch of test warnings that were added recently.
We need to investigate why warnings are not turning into errors.
```
Warnings -----------------------------------------------------------------------
1. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Sepal_Length instead of Sepal.Length as column name
2. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Sepal_Width instead of Sepal.Width as column name
3. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Petal_Length instead of Petal.Length as column name
4. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Petal_Width instead of Petal.Width as column name
Consider adding
importFrom("utils", "object.size")
to your NAMESPACE file.
```
## How was this patch tested?
unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#15560 from felixcheung/rwarnings.
## What changes were proposed in this pull request?
Scala/Python users can add files to Spark job by submit options ```--files``` or ```SparkContext.addFile()```. Meanwhile, users can get the added file by ```SparkFiles.get(filename)```.
We should also support this function for SparkR users, since they also have the requirements for some shared dependency files. For example, SparkR users can download third party R packages to driver firstly, add these files to the Spark job as dependency by this API and then each executor can install these packages by ```install.packages```.
## How was this patch tested?
Add unit test.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#15131 from yanboliang/spark-17577.
## What changes were proposed in this pull request?
This PR tries to add Kolmogorov-Smirnov Test wrapper to SparkR. This wrapper implementation only supports one sample test against normal distribution.
## How was this patch tested?
R unit test.
Author: Junyang Qian <junyangq@databricks.com>
Closes#14881 from junyangq/SPARK-17315.
## What changes were proposed in this pull request?
Add sparkR.version() API.
```
> sparkR.version()
[1] "2.1.0-SNAPSHOT"
```
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#14935 from felixcheung/rsparksessionversion.
## 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.
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?
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?
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?
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?
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?
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?
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.
## What changes were proposed in this pull request?
Add `conf` method to get Runtime Config from SparkSession
## How was this patch tested?
unit tests, manual tests
This is how it works in sparkR shell:
```
SparkSession available as 'spark'.
> conf()
$hive.metastore.warehouse.dir
[1] "file:/opt/spark-2.0.0-bin-hadoop2.6/R/spark-warehouse"
$spark.app.id
[1] "local-1466749575523"
$spark.app.name
[1] "SparkR"
$spark.driver.host
[1] "10.0.2.1"
$spark.driver.port
[1] "45629"
$spark.executorEnv.LD_LIBRARY_PATH
[1] "$LD_LIBRARY_PATH:/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server"
$spark.executor.id
[1] "driver"
$spark.home
[1] "/opt/spark-2.0.0-bin-hadoop2.6"
$spark.master
[1] "local[*]"
$spark.sql.catalogImplementation
[1] "hive"
$spark.submit.deployMode
[1] "client"
> conf("spark.master")
$spark.master
[1] "local[*]"
```
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13885 from felixcheung/rconf.
## What changes were proposed in this pull request?
add union and deprecate unionAll, separate roxygen2 doc for rbind (since their usage and parameter lists are quite different)
`explode` is also deprecated - but seems like replacement is a combination of calls; not sure if we should deprecate it in SparkR, yet.
## How was this patch tested?
unit tests, manual checks for r doc
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13805 from felixcheung/runion.
## What changes were proposed in this pull request?
This PR adds `pivot` function to SparkR for API parity. Since this PR is based on https://github.com/apache/spark/pull/13295 , mhnatiuk should be credited for the work he did.
## How was this patch tested?
Pass the Jenkins tests (including new testcase.)
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13786 from dongjoon-hyun/SPARK-15294.
## What changes were proposed in this pull request?
This PR adds `spark_partition_id` virtual column function in SparkR for API parity.
The following is just an example to illustrate a SparkR usage on a partitioned parquet table created by `spark.range(10).write.mode("overwrite").parquet("/tmp/t1")`.
```r
> collect(select(read.parquet('/tmp/t1'), c('id', spark_partition_id())))
id SPARK_PARTITION_ID()
1 3 0
2 4 0
3 8 1
4 9 1
5 0 2
6 1 3
7 2 4
8 5 5
9 6 6
10 7 7
```
## How was this patch tested?
Pass the Jenkins tests (including new testcase).
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13768 from dongjoon-hyun/SPARK-16053.
## What changes were proposed in this pull request?
This issue adds `read.orc/write.orc` to SparkR for API parity.
## How was this patch tested?
Pass the Jenkins tests (with new testcases).
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13763 from dongjoon-hyun/SPARK-16051.
## What changes were proposed in this pull request?
Add dropTempView and deprecate dropTempTable
## How was this patch tested?
unit tests
shivaram liancheng
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13753 from felixcheung/rdroptempview.
## What changes were proposed in this pull request?
This PR adds `monotonically_increasing_id` column function in SparkR for API parity.
After this PR, SparkR supports the followings.
```r
> df <- read.json("examples/src/main/resources/people.json")
> collect(select(df, monotonically_increasing_id(), df$name, df$age))
monotonically_increasing_id() name age
1 0 Michael NA
2 1 Andy 30
3 2 Justin 19
```
## How was this patch tested?
Pass the Jenkins tests (with added testcase).
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13774 from dongjoon-hyun/SPARK-16059.
## What changes were proposed in this pull request?
This PR introduces the new SparkSession API for SparkR.
`sparkR.session.getOrCreate()` and `sparkR.session.stop()`
"getOrCreate" is a bit unusual in R but it's important to name this clearly.
SparkR implementation should
- SparkSession is the main entrypoint (vs SparkContext; due to limited functionality supported with SparkContext in SparkR)
- SparkSession replaces SQLContext and HiveContext (both a wrapper around SparkSession, and because of API changes, supporting all 3 would be a lot more work)
- Changes to SparkSession is mostly transparent to users due to SPARK-10903
- Full backward compatibility is expected - users should be able to initialize everything just in Spark 1.6.1 (`sparkR.init()`), but with deprecation warning
- Mostly cosmetic changes to parameter list - users should be able to move to `sparkR.session.getOrCreate()` easily
- An advanced syntax with named parameters (aka varargs aka "...") is supported; that should be closer to the Builder syntax that is in Scala/Python (which unfortunately does not work in R because it will look like this: `enableHiveSupport(config(config(master(appName(builder(), "foo"), "local"), "first", "value"), "next, "value"))`
- Updating config on an existing SparkSession is supported, the behavior is the same as Python, in which config is applied to both SparkContext and SparkSession
- Some SparkSession changes are not matched in SparkR, mostly because it would be breaking API change: `catalog` object, `createOrReplaceTempView`
- Other SQLContext workarounds are replicated in SparkR, eg. `tables`, `tableNames`
- `sparkR` shell is updated to use the SparkSession entrypoint (`sqlContext` is removed, just like with Scale/Python)
- All tests are updated to use the SparkSession entrypoint
- A bug in `read.jdbc` is fixed
TODO
- [x] Add more tests
- [ ] Separate PR - update all roxygen2 doc coding example
- [ ] Separate PR - update SparkR programming guide
## How was this patch tested?
unit tests, manual tests
shivaram sun-rui rxin
Author: Felix Cheung <felixcheung_m@hotmail.com>
Author: felixcheung <felixcheung_m@hotmail.com>
Closes#13635 from felixcheung/rsparksession.
## What changes were proposed in this pull request?
This PR adds `randomSplit` to SparkR for API parity.
## How was this patch tested?
Pass the Jenkins tests (with new testcase.)
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13721 from dongjoon-hyun/SPARK-16005.
## What changes were proposed in this pull request?
Add registerTempTable to DataFrame with Deprecate
## How was this patch tested?
unit tests
shivaram liancheng
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13722 from felixcheung/rregistertemptable.
## What changes were proposed in this pull request?
gapply() applies an R function on groups grouped by one or more columns of a DataFrame, and returns a DataFrame. It is like GroupedDataSet.flatMapGroups() in the Dataset API.
Please, let me know what do you think and if you have any ideas to improve it.
Thank you!
## How was this patch tested?
Unit tests.
1. Primitive test with different column types
2. Add a boolean column
3. Compute average by a group
Author: Narine Kokhlikyan <narine.kokhlikyan@gmail.com>
Author: NarineK <narine.kokhlikyan@us.ibm.com>
Closes#12836 from NarineK/gapply2.
