## What changes were proposed in this pull request?
For randomForest classifier, if test data contains unseen labels, it will throw an error. The StringIndexer already has the handleInvalid logic. The patch add a new method to set the underlying StringIndexer handleInvalid logic.
This patch should also apply to other classifiers. This PR focuses on the main logic and randomForest classifier. I will do follow-up PR for other classifiers.
## How was this patch tested?
Add a new unit test based on the error case in the JIRA.
Author: wangmiao1981 <wm624@hotmail.com>
Closes#18496 from wangmiao1981/handle.
## What changes were proposed in this pull request?
Add doc for methods that were left out, and fix various style and consistency issues.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#18493 from actuaryzhang/sparkRDocCleanup.
## What changes were proposed in this pull request?
Grouped documentation for column window methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#18481 from actuaryzhang/sparkRDocWindow.
## What changes were proposed in this pull request?
Grouped documentation for column collection methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>
Closes#18458 from actuaryzhang/sparkRDocCollection.
## What changes were proposed in this pull request?
Grouped documentation for column misc methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>
Closes#18448 from actuaryzhang/sparkRDocMisc.
## What changes were proposed in this pull request?
Grouped documentation for nonaggregate column methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>
Closes#18422 from actuaryzhang/sparkRDocNonAgg.
## What changes were proposed in this pull request?
This PR proposes to support a DDL-formetted string as schema as below:
```r
mockLines <- c("{\"name\":\"Michael\"}",
"{\"name\":\"Andy\", \"age\":30}",
"{\"name\":\"Justin\", \"age\":19}")
jsonPath <- tempfile(pattern = "sparkr-test", fileext = ".tmp")
writeLines(mockLines, jsonPath)
df <- read.df(jsonPath, "json", "name STRING, age DOUBLE")
collect(df)
```
## How was this patch tested?
Tests added in `test_streaming.R` and `test_sparkSQL.R` and manual tests.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#18431 from HyukjinKwon/r-ddl-schema.
## What changes were proposed in this pull request?
Grouped documentation for string column methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>
Closes#18366 from actuaryzhang/sparkRDocString.
## What changes were proposed in this pull request?
Grouped documentation for math column methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>
Closes#18371 from actuaryzhang/sparkRDocMath.
## What changes were proposed in this pull request?
`mcfork` in R looks opening a pipe ahead but the existing logic does not properly close it when it is executed hot. This leads to the failure of more forking due to the limit for number of files open.
This hot execution looks particularly for `gapply`/`gapplyCollect`. For unknown reason, this happens more easily in CentOS and could be reproduced in Mac too.
All the details are described in https://issues.apache.org/jira/browse/SPARK-21093
This PR proposes simply to terminate R's worker processes in the parent of R's daemon to prevent a leak.
## How was this patch tested?
I ran the codes below on both CentOS and Mac with that configuration disabled/enabled.
```r
df <- createDataFrame(list(list(1L, 1, "1", 0.1)), c("a", "b", "c", "d"))
collect(gapply(df, "a", function(key, x) { x }, schema(df)))
collect(gapply(df, "a", function(key, x) { x }, schema(df)))
... # 30 times
```
Also, now it passes R tests on CentOS as below:
```
SparkSQL functions: Spark package found in SPARK_HOME: .../spark
..............................................................................................................................................................
..............................................................................................................................................................
..............................................................................................................................................................
..............................................................................................................................................................
..............................................................................................................................................................
....................................................................................................................................
```
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#18320 from HyukjinKwon/SPARK-21093.
## What changes were proposed in this pull request?
Extend `setJobDescription` to SparkR API.
## How was this patch tested?
It looks difficult to add a test. Manually tested as below:
```r
df <- createDataFrame(iris)
count(df)
setJobDescription("This is an example job.")
count(df)
```
prints ...
![2017-06-22 12 05 49](https://user-images.githubusercontent.com/6477701/27415670-2a649936-5743-11e7-8e95-312f1cd103af.png)
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#18382 from HyukjinKwon/SPARK-21149.
## What changes were proposed in this pull request?
Grouped documentation for datetime column methods.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#18114 from actuaryzhang/sparkRDocDate.
## What changes were proposed in this pull request?
PR https://github.com/apache/spark/pull/17715 Added Constrained Logistic Regression for ML. We should add it to SparkR.
## How was this patch tested?
Add new unit tests.
Author: wangmiao1981 <wm624@hotmail.com>
Closes#18128 from wangmiao1981/test.
## What changes were proposed in this pull request?
Add `stringIndexerOrderType` to `spark.glm` and `spark.survreg` to support string encoding that is consistent with default R.
## How was this patch tested?
new tests
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#18140 from actuaryzhang/sparkRFormula.
## What changes were proposed in this pull request?
LinearSVC should use its own threshold param, rather than the shared one, since it applies to rawPrediction instead of probability. This PR changes the param in the Scala, Python and R APIs.
## How was this patch tested?
New unit test to make sure the threshold can be set to any Double value.
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#18151 from jkbradley/ml-2.2-linearsvc-cleanup.
## What changes were proposed in this pull request?
Grouped documentation for the aggregate functions for Column.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#18025 from actuaryzhang/sparkRDoc4.
## What changes were proposed in this pull request?
Add SQL trunc function
## How was this patch tested?
standard test
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#18291 from actuaryzhang/sparkRTrunc2.
## What changes were proposed in this pull request?
This PR proposes to list the files in test _after_ removing both "spark-warehouse" and "metastore_db" so that the next run of R tests pass fine. This is sometimes a bit annoying.
## How was this patch tested?
Manually running multiple times R tests via `./R/run-tests.sh`.
**Before**
Second run:
```
SparkSQL functions: Spark package found in SPARK_HOME: .../spark
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
....................................................................................................1234.......................
Failed -------------------------------------------------------------------------
1. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3384)
length(list1) not equal to length(list2).
1/1 mismatches
[1] 25 - 23 == 2
2. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3384)
sort(list1, na.last = TRUE) not equal to sort(list2, na.last = TRUE).
10/25 mismatches
x[16]: "metastore_db"
y[16]: "pkg"
x[17]: "pkg"
y[17]: "R"
x[18]: "R"
y[18]: "README.md"
x[19]: "README.md"
y[19]: "run-tests.sh"
x[20]: "run-tests.sh"
y[20]: "SparkR_2.2.0.tar.gz"
x[21]: "metastore_db"
y[21]: "pkg"
x[22]: "pkg"
y[22]: "R"
x[23]: "R"
y[23]: "README.md"
x[24]: "README.md"
y[24]: "run-tests.sh"
x[25]: "run-tests.sh"
y[25]: "SparkR_2.2.0.tar.gz"
3. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3388)
length(list1) not equal to length(list2).
1/1 mismatches
[1] 25 - 23 == 2
4. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3388)
sort(list1, na.last = TRUE) not equal to sort(list2, na.last = TRUE).
10/25 mismatches
x[16]: "metastore_db"
y[16]: "pkg"
x[17]: "pkg"
y[17]: "R"
x[18]: "R"
y[18]: "README.md"
x[19]: "README.md"
y[19]: "run-tests.sh"
x[20]: "run-tests.sh"
y[20]: "SparkR_2.2.0.tar.gz"
x[21]: "metastore_db"
y[21]: "pkg"
x[22]: "pkg"
y[22]: "R"
x[23]: "R"
y[23]: "README.md"
x[24]: "README.md"
y[24]: "run-tests.sh"
x[25]: "run-tests.sh"
y[25]: "SparkR_2.2.0.tar.gz"
DONE ===========================================================================
```
**After**
Second run:
```
SparkSQL functions: Spark package found in SPARK_HOME: .../spark
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................
```
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#18335 from HyukjinKwon/SPARK-21128.
## What changes were proposed in this pull request?
Update Running R Tests dependence packages to:
```bash
R -e "install.packages(c('knitr', 'rmarkdown', 'testthat', 'e1071', 'survival'), repos='http://cran.us.r-project.org')"
```
## How was this patch tested?
manual tests
Author: Yuming Wang <wgyumg@gmail.com>
Closes#18271 from wangyum/building-spark.
### What changes were proposed in this pull request?
The current option name `wholeFile` is misleading for CSV users. Currently, it is not representing a record per file. Actually, one file could have multiple records. Thus, we should rename it. Now, the proposal is `multiLine`.
### How was this patch tested?
N/A
Author: Xiao Li <gatorsmile@gmail.com>
Closes#18202 from gatorsmile/renameCVSOption.
## What changes were proposed in this pull request?
clean up after big test move
## How was this patch tested?
unit tests, jenkins
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#18267 from felixcheung/rtestset2.
## What changes were proposed in this pull request?
Move all existing tests to non-installed directory so that it will never run by installing SparkR package
For a follow-up PR:
- remove all skip_on_cran() calls in tests
- clean up test timer
- improve or change basic tests that do run on CRAN (if anyone has suggestion)
It looks like `R CMD build pkg` will still put pkg\tests (ie. the full tests) into the source package but `R CMD INSTALL` on such source package does not install these tests (and so `R CMD check` does not run them)
## How was this patch tested?
- [x] unit tests, Jenkins
- [x] AppVeyor
- [x] make a source package, install it, `R CMD check` it - verify the full tests are not installed or run
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#18264 from felixcheung/rtestset.
## What changes were proposed in this pull request?
Document Dataset.union is resolution by position, not by name, since this has been a confusing point for a lot of users.
## How was this patch tested?
N/A - doc only change.
Author: Reynold Xin <rxin@databricks.com>
Closes#18256 from rxin/SPARK-21042.
## What changes were proposed in this pull request?
to investigate how long they run
## How was this patch tested?
Jenkins, AppVeyor
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#18104 from felixcheung/rtimetest.
## What changes were proposed in this pull request?
1, add an example for sparkr `decisionTree`
2, document it in user guide
## How was this patch tested?
local submit
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#18067 from zhengruifeng/dt_example.
## What changes were proposed in this pull request?
Joint coefficients with intercept for SparkR linear SVM summary.
## How was this patch tested?
Existing tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#18035 from yanboliang/svm-r.
## What changes were proposed in this pull request?
This change skips tests that use the Hadoop libraries while running
on CRAN check with Windows as the operating system. This is to handle
cases where the Hadoop winutils binaries are missing on the target
system. The skipped tests consist of
1. Tests that save, load a model in MLlib
2. Tests that save, load CSV, JSON and Parquet files in SQL
3. Hive tests
## How was this patch tested?
Tested by running on a local windows VM with HADOOP_HOME unset. Also testing with https://win-builder.r-project.org
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#17966 from shivaram/sparkr-windows-cran.
## What changes were proposed in this pull request?
support decision tree in R
## How was this patch tested?
added tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#17981 from zhengruifeng/dt_r.
## What changes were proposed in this pull request?
Some examples in the DataFrame methods are syntactically wrong, even though they are pseudo code. Fix these and some style issues.
Author: Wayne Zhang <actuaryzhang@uber.com>
Closes#18003 from actuaryzhang/sparkRDoc3.
## What changes were proposed in this pull request?
Rename `carsDF` to `df` in SparkR `rollup` and `cube` examples.
## How was this patch tested?
Manual tests.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17988 from zero323/cube-docs.
## What changes were proposed in this pull request?
- Adds R wrapper for `o.a.s.sql.functions.broadcast`.
- Renames `broadcast` to `broadcast_`.
## How was this patch tested?
Unit tests, check `check-cran.sh`.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17965 from zero323/SPARK-20726.
## What changes were proposed in this pull request?
This PR proposes three things as below:
- Use casting rules to a timestamp in `to_timestamp` by default (it was `yyyy-MM-dd HH:mm:ss`).
- Support single argument for `to_timestamp` similarly with APIs in other languages.
For example, the one below works
```
import org.apache.spark.sql.functions._
Seq("2016-12-31 00:12:00.00").toDF("a").select(to_timestamp(col("a"))).show()
```
prints
```
+----------------------------------------+
|to_timestamp(`a`, 'yyyy-MM-dd HH:mm:ss')|
+----------------------------------------+
| 2016-12-31 00:12:00|
+----------------------------------------+
```
whereas this does not work in SQL.
**Before**
```
spark-sql> SELECT to_timestamp('2016-12-31 00:12:00');
Error in query: Invalid number of arguments for function to_timestamp; line 1 pos 7
```
**After**
```
spark-sql> SELECT to_timestamp('2016-12-31 00:12:00');
2016-12-31 00:12:00
```
- Related document improvement for SQL function descriptions and other API descriptions accordingly.
**Before**
```
spark-sql> DESCRIBE FUNCTION extended to_date;
...
Usage: to_date(date_str, fmt) - Parses the `left` expression with the `fmt` expression. Returns null with invalid input.
Extended Usage:
Examples:
> SELECT to_date('2016-12-31', 'yyyy-MM-dd');
2016-12-31
```
```
spark-sql> DESCRIBE FUNCTION extended to_timestamp;
...
Usage: to_timestamp(timestamp, fmt) - Parses the `left` expression with the `format` expression to a timestamp. Returns null with invalid input.
Extended Usage:
Examples:
> SELECT to_timestamp('2016-12-31', 'yyyy-MM-dd');
2016-12-31 00:00:00.0
```
**After**
```
spark-sql> DESCRIBE FUNCTION extended to_date;
...
Usage:
to_date(date_str[, fmt]) - Parses the `date_str` expression with the `fmt` expression to
a date. Returns null with invalid input. By default, it follows casting rules to a date if
the `fmt` is omitted.
Extended Usage:
Examples:
> SELECT to_date('2009-07-30 04:17:52');
2009-07-30
> SELECT to_date('2016-12-31', 'yyyy-MM-dd');
2016-12-31
```
```
spark-sql> DESCRIBE FUNCTION extended to_timestamp;
...
Usage:
to_timestamp(timestamp[, fmt]) - Parses the `timestamp` expression with the `fmt` expression to
a timestamp. Returns null with invalid input. By default, it follows casting rules to
a timestamp if the `fmt` is omitted.
Extended Usage:
Examples:
> SELECT to_timestamp('2016-12-31 00:12:00');
2016-12-31 00:12:00
> SELECT to_timestamp('2016-12-31', 'yyyy-MM-dd');
2016-12-31 00:00:00
```
## How was this patch tested?
Added tests in `datetime.sql`.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17901 from HyukjinKwon/to_timestamp_arg.
## What changes were proposed in this pull request?
- [x] need to test by running R CMD check --as-cran
- [x] sanity check vignettes
## How was this patch tested?
Jenkins
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17945 from felixcheung/rchangesforpackage.
## What changes were proposed in this pull request?
Change it to check for relative count like in this test https://github.com/apache/spark/blame/master/R/pkg/inst/tests/testthat/test_sparkSQL.R#L3355 for catalog APIs
## How was this patch tested?
unit tests, this needs to combine with another commit with SQL change to check
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17905 from felixcheung/rtabletests.
## What changes were proposed in this pull request?
Cleaning existing temp tables before running tableNames tests
## How was this patch tested?
SparkR Unit tests
Author: Hossein <hossein@databricks.com>
Closes#17903 from falaki/SPARK-20661.
## What changes were proposed in this pull request?
Fix typo in vignettes
Author: Wayne Zhang <actuaryzhang@uber.com>
Closes#17884 from actuaryzhang/typo.
## What changes were proposed in this pull request?
set timezone on windows
## How was this patch tested?
unit test, AppVeyor
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17892 from felixcheung/rtimestamptest.
## What changes were proposed in this pull request?
- Add SparkR wrapper for `Dataset.alias`.
- Adjust roxygen annotations for `functions.alias` (including example usage).
## How was this patch tested?
Unit tests, `check_cran.sh`.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17825 from zero323/SPARK-20550.
## What changes were proposed in this pull request?
add environment
## How was this patch tested?
wait for appveyor run
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17878 from felixcheung/appveyorrcran.
## What changes were proposed in this pull request?
Make tests more reliable by having it till processed.
Increasing timeout value might help but ultimately the flakiness from processing delay when Jenkins is hard to account for. This isn't an actual public API supported
## How was this patch tested?
unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17857 from felixcheung/rsstestrelia.
## What changes were proposed in this pull request?
Adds wrapper for `o.a.s.sql.functions.input_file_name`
## How was this patch tested?
Existing unit tests, additional unit tests, `check-cran.sh`.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17818 from zero323/SPARK-20544.
## What changes were proposed in this pull request?
Adds support for generic hints on `SparkDataFrame`
## How was this patch tested?
Unit tests, `check-cran.sh`
Author: zero323 <zero323@users.noreply.github.com>
Closes#17851 from zero323/SPARK-20585.
## What changes were proposed in this pull request?
Add
- R vignettes
- R programming guide
- SS programming guide
- R example
Also disable spark.als in vignettes for now since it's failing (SPARK-20402)
## How was this patch tested?
manually
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17814 from felixcheung/rdocss.
## What changes were proposed in this pull request?
General rule on skip or not:
skip if
- RDD tests
- tests could run long or complicated (streaming, hivecontext)
- tests on error conditions
- tests won't likely change/break
## How was this patch tested?
unit tests, `R CMD check --as-cran`, `R CMD check`
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17817 from felixcheung/rskiptest.
## What changes were proposed in this pull request?
doc only
## How was this patch tested?
manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17828 from felixcheung/rnotfamily.
## What changes were proposed in this pull request?
Adds R wrappers for:
- `o.a.s.sql.functions.grouping` as `o.a.s.sql.functions.is_grouping` (to avoid shading `base::grouping`
- `o.a.s.sql.functions.grouping_id`
## How was this patch tested?
Existing unit tests, additional unit tests. `check-cran.sh`.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17807 from zero323/SPARK-20532.
## What changes were proposed in this pull request?
Add without param for timeout - will need this to submit a job that runs until stopped
Need this for 2.2
## How was this patch tested?
manually, unit test
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17815 from felixcheung/rssawaitinfinite.
## What changes were proposed in this pull request?
- Add null-safe equality operator `%<=>%` (sames as `o.a.s.sql.Column.eqNullSafe`, `o.a.s.sql.Column.<=>`)
- Add boolean negation operator `!` and function `not `.
## How was this patch tested?
Existing unit tests, additional unit tests, `check-cran.sh`.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17783 from zero323/SPARK-20490.
## What changes were proposed in this pull request?
Ad R wrappers for
- `o.a.s.sql.functions.explode_outer`
- `o.a.s.sql.functions.posexplode_outer`
## How was this patch tested?
Additional unit tests, manual testing.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17809 from zero323/SPARK-20535.
## What changes were proposed in this pull request?
It seems we are using `SQLUtils.getSQLDataType` for type string in structField. It looks we can replace this with `CatalystSqlParser.parseDataType`.
They look similar DDL-like type definitions as below:
```scala
scala> Seq(Tuple1(Tuple1("a"))).toDF.show()
```
```
+---+
| _1|
+---+
|[a]|
+---+
```
```scala
scala> Seq(Tuple1(Tuple1("a"))).toDF.select($"_1".cast("struct<_1:string>")).show()
```
```
+---+
| _1|
+---+
|[a]|
+---+
```
Such type strings looks identical when R’s one as below:
```R
> write.df(sql("SELECT named_struct('_1', 'a') as struct"), "/tmp/aa", "parquet")
> collect(read.df("/tmp/aa", "parquet", structType(structField("struct", "struct<_1:string>"))))
struct
1 a
```
R’s one is stricter because we are checking the types via regular expressions in R side ahead.
Actual logics there look a bit different but as we check it ahead in R side, it looks replacing it would not introduce (I think) no behaviour changes. To make this sure, the tests dedicated for it were added in SPARK-20105. (It looks `structField` is the only place that calls this method).
## How was this patch tested?
Existing tests - https://github.com/apache/spark/blob/master/R/pkg/inst/tests/testthat/test_sparkSQL.R#L143-L194 should cover this.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17785 from HyukjinKwon/SPARK-20493.
## What changes were proposed in this pull request?
Replace
note repeat_string 2.3.0
with
note repeat_string since 2.3.0
## How was this patch tested?
`create-docs.sh`
Author: zero323 <zero323@users.noreply.github.com>
Closes#17779 from zero323/REPEAT-NOTE.
## What changes were proposed in this pull request?
Some PySpark & SparkR tests run with tiny dataset and tiny ```maxIter```, which means they are not converged. I don’t think checking intermediate result during iteration make sense, and these intermediate result may vulnerable and not stable, so we should switch to check the converged result. We hit this issue at #17746 when we upgrade breeze to 0.13.1.
## How was this patch tested?
Existing tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#17757 from yanboliang/flaky-test.
## What changes were proposed in this pull request?
- Add `rollup` and `cube` methods and corresponding generics.
- Add short description to the vignette.
## How was this patch tested?
- Existing unit tests.
- Additional unit tests covering new features.
- `check-cran.sh`.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17728 from zero323/SPARK-20437.
## What changes were proposed in this pull request?
Upgrade breeze version to 0.13.1, which fixed some critical bugs of L-BFGS-B.
## How was this patch tested?
Existing unit tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#17746 from yanboliang/spark-20449.
## 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?
Checking a source parameter is asynchronous. When the query is created, it's not guaranteed that source has been created. This PR just increases the timeout of awaitTermination to ensure the parsing error is thrown.
## How was this patch tested?
Jenkins
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#17687 from zsxwing/SPARK-20397.
## What changes were proposed in this pull request?
Document fpGrowth in:
- vignettes
- programming guide
- code example
## How was this patch tested?
Manual tests.
Author: zero323 <zero323@users.noreply.github.com>
Closes#17557 from zero323/SPARK-20208.
## What changes were proposed in this pull request?
This was suggested to be `as.json.array` at the first place in the PR to SPARK-19828 but we could not do this as the lint check emits an error for multiple dots in the variable names.
After SPARK-20278, now we are able to use `multiple.dots.in.names`. `asJsonArray` in `from_json` function is still able to be changed as 2.2 is not released yet.
So, this PR proposes to rename `asJsonArray` to `as.json.array`.
## How was this patch tested?
Jenkins tests, local tests with `./R/run-tests.sh` and manual `./dev/lint-r`. Existing tests should cover this.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17653 from HyukjinKwon/SPARK-19828-followup.
## What changes were proposed in this pull request?
Currently, multi-dot separated variables in R is not allowed. For example,
```diff
setMethod("from_json", signature(x = "Column", schema = "structType"),
- function(x, schema, asJsonArray = FALSE, ...) {
+ function(x, schema, as.json.array = FALSE, ...) {
if (asJsonArray) {
jschema <- callJStatic("org.apache.spark.sql.types.DataTypes",
"createArrayType",
```
produces an error as below:
```
R/functions.R:2462:31: style: Words within variable and function names should be separated by '_' rather than '.'.
function(x, schema, as.json.array = FALSE, ...) {
^~~~~~~~~~~~~
```
This seems against https://google.github.io/styleguide/Rguide.xml#identifiers which says
> The preferred form for variable names is all lower case letters and words separated with dots
This looks because lintr by default https://github.com/jimhester/lintr follows http://r-pkgs.had.co.nz/style.html as written in the README.md. Few cases seems not following Google's one as "a few tweaks".
Per [SPARK-6813](https://issues.apache.org/jira/browse/SPARK-6813), we follow Google's R Style Guide with few exceptions https://google.github.io/styleguide/Rguide.xml. This is also merged into Spark's website - https://github.com/apache/spark-website/pull/43
Also, it looks we have no limit on function name. This rule also looks affecting to the name of functions as written in the README.md.
> `multiple_dots_linter`: check that function and variable names are separated by _ rather than ..
## How was this patch tested?
Manually tested `./dev/lint-r`with the manual change below in `R/functions.R`:
```diff
setMethod("from_json", signature(x = "Column", schema = "structType"),
- function(x, schema, asJsonArray = FALSE, ...) {
+ function(x, schema, as.json.array = FALSE, ...) {
if (asJsonArray) {
jschema <- callJStatic("org.apache.spark.sql.types.DataTypes",
"createArrayType",
```
**Before**
```R
R/functions.R:2462:31: style: Words within variable and function names should be separated by '_' rather than '.'.
function(x, schema, as.json.array = FALSE, ...) {
^~~~~~~~~~~~~
```
**After**
```
lintr checks passed.
```
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17590 from HyukjinKwon/disable-dot-in-name.
## What changes were proposed in this pull request?
Fixed spelling of "charactor"
## How was this patch tested?
Spelling change only
Author: Brendan Dwyer <brendan.dwyer@ibm.com>
Closes#17611 from bdwyer2/SPARK-20298.
## What changes were proposed in this pull request?
Test failed because SPARK_HOME is not set before Spark is installed.
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17516 from felixcheung/rdircheckincran.
## 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?
Update doc to remove external for createTable, add refreshByPath in python
## How was this patch tested?
manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17512 from felixcheung/catalogdoc.
## What changes were proposed in this pull request?
minor update
zero323
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17526 from felixcheung/rfpgrowthfollowup.
## What changes were proposed in this pull request?
It seems cran check scripts corrects `R/pkg/DESCRIPTION` and follows the order in `Collate` fields.
This PR proposes to fix `catalog.R`'s order so that running this script does not show up a small diff in this file every time.
## How was this patch tested?
Manually via `./R/check-cran.sh`.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17528 from HyukjinKwon/minor-reorder-description.
## 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.
JIRA Issue: https://issues.apache.org/jira/browse/SPARK-20123
## What changes were proposed in this pull request?
If $SPARK_HOME or $FWDIR variable contains spaces, then use "./dev/make-distribution.sh --name custom-spark --tgz -Psparkr -Phadoop-2.7 -Phive -Phive-thriftserver -Pmesos -Pyarn" build spark will failed.
## How was this patch tested?
manual tests
Author: zuotingbing <zuo.tingbing9@zte.com.cn>
Closes#17452 from zuotingbing/spark-bulid.
## What changes were proposed in this pull request?
It seems `checkType` and the type string in `structField` are not being tested closely. This string format currently seems SparkR-specific (see d1f6c64c4b/sql/core/src/main/scala/org/apache/spark/sql/api/r/SQLUtils.scala (L93-L131)) but resembles SQL type definition.
Therefore, it seems nicer if we test positive/negative cases in R side.
## How was this patch tested?
Unit tests in `test_sparkSQL.R`.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17439 from HyukjinKwon/r-typestring-tests.
## What changes were proposed in this pull request?
This PR proposes to match minor documentations changes in https://github.com/apache/spark/pull/17399 and https://github.com/apache/spark/pull/17380 to R/Python.
## How was this patch tested?
Manual tests in Python , Python tests via `./python/run-tests.py --module=pyspark-sql` and lint-checks for Python/R.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17429 from HyukjinKwon/minor-match-doc.
## What changes were proposed in this pull request?
SparkR ```spark.getSparkFiles``` fails when it was called on executors, see details at [SPARK-19925](https://issues.apache.org/jira/browse/SPARK-19925).
## How was this patch tested?
Add unit tests, and verify this fix at standalone and yarn cluster.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#17274 from yanboliang/spark-19925.
## What changes were proposed in this pull request?
When SparkR is installed as a R package there might not be any java runtime.
If it is not there SparkR's `sparkR.session()` will block waiting for the connection timeout, hanging the R IDE/shell, without any notification or message.
## How was this patch tested?
manually
- [x] need to test on Windows
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16596 from felixcheung/rcheckjava.
## What changes were proposed in this pull request?
Update docs for NaN handling in approxQuantile.
## How was this patch tested?
existing tests.
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#17369 from zhengruifeng/doc_quantiles_nan.
## What changes were proposed in this pull request?
Currently JSON and CSV have exactly the same logic about handling bad records, this PR tries to abstract it and put it in a upper level to reduce code duplication.
The overall idea is, we make the JSON and CSV parser to throw a BadRecordException, then the upper level, FailureSafeParser, handles bad records according to the parse mode.
Behavior changes:
1. with PERMISSIVE mode, if the number of tokens doesn't match the schema, previously CSV parser will treat it as a legal record and parse as many tokens as possible. After this PR, we treat it as an illegal record, and put the raw record string in a special column, but we still parse as many tokens as possible.
2. all logging is removed as they are not very useful in practice.
## How was this patch tested?
existing tests
Author: Wenchen Fan <wenchen@databricks.com>
Author: hyukjinkwon <gurwls223@gmail.com>
Author: Wenchen Fan <cloud0fan@gmail.com>
Closes#17315 from cloud-fan/bad-record2.
## What changes were proposed in this pull request?
doc only change
## How was this patch tested?
manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17356 from felixcheung/rdfcheckpoint2.
## 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?
This PR proposes to support an array of struct type in `to_json` as below:
```scala
import org.apache.spark.sql.functions._
val df = Seq(Tuple1(Tuple1(1) :: Nil)).toDF("a")
df.select(to_json($"a").as("json")).show()
```
```
+----------+
| json|
+----------+
|[{"_1":1}]|
+----------+
```
Currently, it throws an exception as below (a newline manually inserted for readability):
```
org.apache.spark.sql.AnalysisException: cannot resolve 'structtojson(`array`)' due to data type
mismatch: structtojson requires that the expression is a struct expression.;;
```
This allows the roundtrip with `from_json` as below:
```scala
import org.apache.spark.sql.functions._
import org.apache.spark.sql.types._
val schema = ArrayType(StructType(StructField("a", IntegerType) :: Nil))
val df = Seq("""[{"a":1}, {"a":2}]""").toDF("json").select(from_json($"json", schema).as("array"))
df.show()
// Read back.
df.select(to_json($"array").as("json")).show()
```
```
+----------+
| array|
+----------+
|[[1], [2]]|
+----------+
+-----------------+
| json|
+-----------------+
|[{"a":1},{"a":2}]|
+-----------------+
```
Also, this PR proposes to rename from `StructToJson` to `StructsToJson ` and `JsonToStruct` to `JsonToStructs`.
## How was this patch tested?
Unit tests in `JsonFunctionsSuite` and `JsonExpressionsSuite` for Scala, doctest for Python and test in `test_sparkSQL.R` for R.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17192 from HyukjinKwon/SPARK-19849.
## What changes were proposed in this pull request?
Passes R `tempdir()` (this is the R session temp dir, shared with other temp files/dirs) to JVM, set System.Property for derby home dir to move derby.log
## How was this patch tested?
Manually, unit tests
With this, these are relocated to under /tmp
```
# ls /tmp/RtmpG2M0cB/
derby.log
```
And they are removed automatically when the R session is ended.
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16330 from felixcheung/rderby.
## What changes were proposed in this pull request?
It seems cran check scripts corrects `R/pkg/DESCRIPTION` and follows the order in `Collate` fields.
This PR proposes to fix this so that running this script does not show up a diff in this file.
## How was this patch tested?
Manually via `./R/check-cran.sh`.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17349 from HyukjinKwon/minor-cran.
## 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?
Since we could not directly define the array type in R, this PR proposes to support array types in R as string types that are used in `structField` as below:
```R
jsonArr <- "[{\"name\":\"Bob\"}, {\"name\":\"Alice\"}]"
df <- as.DataFrame(list(list("people" = jsonArr)))
collect(select(df, alias(from_json(df$people, "array<struct<name:string>>"), "arrcol")))
```
prints
```R
arrcol
1 Bob, Alice
```
## How was this patch tested?
Unit tests in `test_sparkSQL.R`.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#17178 from HyukjinKwon/SPARK-19828.
## What changes were proposed in this pull request?
Port Tweedie GLM #16344 to SparkR
felixcheung yanboliang
## How was this patch tested?
new test in SparkR
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#16729 from actuaryzhang/sparkRTweedie.
## What changes were proposed in this pull request?
RandomForest R Wrapper and GBT R Wrapper return param `maxDepth` to R models.
Below 4 R wrappers are changed:
* `RandomForestClassificationWrapper`
* `RandomForestRegressionWrapper`
* `GBTClassificationWrapper`
* `GBTRegressionWrapper`
## How was this patch tested?
Test manually on my local machine.
Author: Xin Ren <iamshrek@126.com>
Closes#17207 from keypointt/SPARK-19282.
### What changes were proposed in this pull request?
Observed by felixcheung in https://github.com/apache/spark/pull/16739, when users use the shuffle-enabled `repartition` API, they expect the partition they got should be the exact number they provided, even if they call shuffle-disabled `coalesce` later.
Currently, `CollapseRepartition` rule does not consider whether shuffle is enabled or not. Thus, we got the following unexpected result.
```Scala
val df = spark.range(0, 10000, 1, 5)
val df2 = df.repartition(10)
assert(df2.coalesce(13).rdd.getNumPartitions == 5)
assert(df2.coalesce(7).rdd.getNumPartitions == 5)
assert(df2.coalesce(3).rdd.getNumPartitions == 3)
```
This PR is to fix the issue. We preserve shuffle-enabled Repartition.
### How was this patch tested?
Added a test case
Author: Xiao Li <gatorsmile@gmail.com>
Closes#16933 from gatorsmile/CollapseRepartition.
## What changes were proposed in this pull request?
Added checks for name consistency of input data frames in union.
## How was this patch tested?
new test.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#17159 from actuaryzhang/sparkRUnion.
## 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?
Update R document to use JDK8.
## How was this patch tested?
manual tests
Author: Yuming Wang <wgyumg@gmail.com>
Closes#17162 from wangyum/SPARK-19550.
## What changes were proposed in this pull request?
Update doc for R, programming guide. Clarify default behavior for all languages.
## How was this patch tested?
manually
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#17128 from felixcheung/jsonwholefiledoc.
Update R doc:
1. columns, names and colnames returns a vector of strings, not **list** as in current doc.
2. `colnames<-` does allow the subset assignment, so the length of `value` can be less than the number of columns, e.g., `colnames(df)[1] <- "a"`.
felixcheung
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#17115 from actuaryzhang/sparkRMinorDoc.
## What changes were proposed in this pull request?
Replace `iris` dataset with `Titanic` or other dataset in example and document.
## How was this patch tested?
Manual and existing test
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#17032 from wangmiao1981/example.
## What changes were proposed in this pull request?
The `[[` method is supposed to take a single index and return a column. This is different from base R which takes a vector index. We should check for this and issue warning or error when vector index is supplied (which is very likely given the behavior in base R).
Currently I'm issuing a warning message and just take the first element of the vector index. We could change this to an error it that's better.
## How was this patch tested?
new tests
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#17017 from actuaryzhang/sparkRSubsetter.
## What changes were proposed in this pull request?
This is a follow-up PR of #16800
When doing SPARK-19456, we found that "" should be consider a NULL column name and should not be set. aggregationDepth should be exposed as an expert parameter.
## How was this patch tested?
Existing tests.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16945 from wangmiao1981/svc.
## What changes were proposed in this pull request?
We recently add the spark.svmLinear API for SparkR. We need to add an example and update the vignettes.
## How was this patch tested?
Manually run example.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16969 from wangmiao1981/example.
## What changes were proposed in this pull request?
SparkR ```approxQuantile``` supports input multiple columns.
## How was this patch tested?
Unit test.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16951 from yanboliang/spark-19619.
## 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 is cause by changes in SPARK-18444, SPARK-18643 that we no longer install Spark when `master = ""` (default), but also related to SPARK-18449 since the real `master` value is not known at the time the R code in `sparkR.session` is run. (`master` cannot default to "local" since it could be overridden by spark-submit commandline or spark config)
- as a result, while running SparkR as a package in IDE is working fine, CRAN check is not as it is launching it via non-interactive script
- fix is to add check to the beginning of each test and vignettes; the same would also work by changing `sparkR.session()` to `sparkR.session(master = "local")` in tests, but I think being more explicit is better.
## How was this patch tested?
Tested this by reverting version to 2.1, since it needs to download the release jar with matching version. But since there are changes in 2.2 (specifically around SparkR ML) that are incompatible with 2.1, some tests are failing in this config. Will need to port this to branch-2.1 and retest with 2.1 release jar.
manually as:
```
# modify DESCRIPTION to revert version to 2.1.0
SPARK_HOME=/usr/spark R CMD build pkg
# run cran check without SPARK_HOME
R CMD check --as-cran SparkR_2.1.0.tar.gz
```
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16720 from felixcheung/rcranchecktest.
## What changes were proposed in this pull request?
Fix a bug in collect method for collecting timestamp column, the bug can be reproduced as shown in the following codes and outputs:
```
library(SparkR)
sparkR.session(master = "local")
df <- data.frame(col1 = c(0, 1, 2),
col2 = c(as.POSIXct("2017-01-01 00:00:01"), NA, as.POSIXct("2017-01-01 12:00:01")))
sdf1 <- createDataFrame(df)
print(dtypes(sdf1))
df1 <- collect(sdf1)
print(lapply(df1, class))
sdf2 <- filter(sdf1, "col1 > 0")
print(dtypes(sdf2))
df2 <- collect(sdf2)
print(lapply(df2, class))
```
As we can see from the printed output, the column type of col2 in df2 is converted to numeric unexpectedly, when NA exists at the top of the column.
This is caused by method `do.call(c, list)`, if we convert a list, i.e. `do.call(c, list(NA, as.POSIXct("2017-01-01 12:00:01"))`, the class of the result is numeric instead of POSIXct.
Therefore, we need to cast the data type of the vector explicitly.
## How was this patch tested?
The patch can be tested manually with the same code above.
Author: titicaca <fangzhou.yang@hotmail.com>
Closes#16689 from titicaca/sparkr-dev.
## What changes were proposed in this pull request?
After SPARK-19464, **SparkPullRequestBuilder** fails because it still tries to use hadoop2.3.
**BEFORE**
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/72595/console
```
========================================================================
Building Spark
========================================================================
[error] Could not find hadoop2.3 in the list. Valid options are ['hadoop2.6', 'hadoop2.7']
Attempting to post to Github...
> Post successful.
```
**AFTER**
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/72595/console
```
========================================================================
Building Spark
========================================================================
[info] Building Spark (w/Hive 1.2.1) using SBT with these arguments: -Phadoop-2.6 -Pmesos -Pkinesis-asl -Pyarn -Phive-thriftserver -Phive test:package streaming-kafka-0-8-assembly/assembly streaming-flume-assembly/assembly streaming-kinesis-asl-assembly/assembly
Using /usr/java/jdk1.8.0_60 as default JAVA_HOME.
Note, this will be overridden by -java-home if it is set.
```
## How was this patch tested?
Pass the existing test.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#16858 from dongjoon-hyun/hotfix_run-tests.
## 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?
The names method fails to check for validity of the assignment values. This can be fixed by calling colnames within names.
## How was this patch tested?
new tests.
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#16794 from actuaryzhang/sparkRNames.
## What changes were proposed in this pull request?
Current version has error in vignettes:
```
model <- spark.bisectingKmeans(df, Sepal_Length ~ Sepal_Width, k = 4)
summary(kmeansModel)
```
`kmeansModel` does not exist...
felixcheung wangmiao1981
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#16799 from actuaryzhang/sparkRVignettes.
## What changes were proposed in this pull request?
Update programming guide, example and vignette with Bisecting k-means.
Author: krishnakalyan3 <krishnakalyan3@gmail.com>
Closes#16767 from krishnakalyan3/bisecting-kmeans.
## What changes were proposed in this pull request
When Kmeans using initMode = "random" and some random seed, it is possible the actual cluster size doesn't equal to the configured `k`.
In this case, summary(model) returns error due to the number of cols of coefficient matrix doesn't equal to k.
Example:
> col1 <- c(1, 2, 3, 4, 0, 1, 2, 3, 4, 0)
> col2 <- c(1, 2, 3, 4, 0, 1, 2, 3, 4, 0)
> col3 <- c(1, 2, 3, 4, 0, 1, 2, 3, 4, 0)
> cols <- as.data.frame(cbind(col1, col2, col3))
> df <- createDataFrame(cols)
>
> model2 <- spark.kmeans(data = df, ~ ., k = 5, maxIter = 10, initMode = "random", seed = 22222, tol = 1E-5)
>
> summary(model2)
Error in `colnames<-`(`*tmp*`, value = c("col1", "col2", "col3")) :
length of 'dimnames' [2] not equal to array extent
In addition: Warning message:
In matrix(coefficients, ncol = k) :
data length [9] is not a sub-multiple or multiple of the number of rows [2]
Fix: Get the actual cluster size in the summary and use it to build the coefficient matrix.
## How was this patch tested?
Add unit tests.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16666 from wangmiao1981/kmeans.
## What changes were proposed in this pull request?
The `coefficients` component in model summary should be 'matrix' but the underlying structure is indeed list. This affects several models except for 'AFTSurvivalRegressionModel' which has the correct implementation. The fix is to first `unlist` the coefficients returned from the `callJMethod` before converting to matrix. An example illustrates the issues:
```
data(iris)
df <- createDataFrame(iris)
model <- spark.glm(df, Sepal_Length ~ Sepal_Width, family = "gaussian")
s <- summary(model)
> str(s$coefficients)
List of 8
$ : num 6.53
$ : num -0.223
$ : num 0.479
$ : num 0.155
$ : num 13.6
$ : num -1.44
$ : num 0
$ : num 0.152
- attr(*, "dim")= int [1:2] 2 4
- attr(*, "dimnames")=List of 2
..$ : chr [1:2] "(Intercept)" "Sepal_Width"
..$ : chr [1:4] "Estimate" "Std. Error" "t value" "Pr(>|t|)"
> s$coefficients[, 2]
$`(Intercept)`
[1] 0.4788963
$Sepal_Width
[1] 0.1550809
```
This shows that the underlying structure of coefficients is still `list`.
felixcheung wangmiao1981
Author: actuaryzhang <actuaryzhang10@gmail.com>
Closes#16730 from actuaryzhang/sparkRCoef.
## What changes were proposed in this pull request?
With extract `[[` or replace `[[<-`, the parameter `i` is a column index, that needs to be corrected in doc. Also a few minor updates: examples, links.
## How was this patch tested?
manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16721 from felixcheung/rsubsetdoc.
## What changes were proposed in this pull request?
This affects mostly running job from the driver in client mode when results are expected to be through stdout (which should be somewhat rare, but possible)
Before:
```
> a <- as.DataFrame(cars)
> b <- group_by(a, "dist")
> c <- count(b)
> sparkR.callJMethod(c$countjc, "explain", TRUE)
NULL
```
After:
```
> a <- as.DataFrame(cars)
> b <- group_by(a, "dist")
> c <- count(b)
> sparkR.callJMethod(c$countjc, "explain", TRUE)
count#11L
NULL
```
Now, `column.explain()` doesn't seem very useful (we can get more extensive output with `DataFrame.explain()`) but there are other more complex examples with calls of `println` in Scala/JVM side, that are getting dropped.
## How was this patch tested?
manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16670 from felixcheung/rjvmstdout.
## What changes were proposed in this pull request?
add header
## How was this patch tested?
Manual run to check vignettes html is created properly
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16709 from felixcheung/rfilelicense.
## What changes were proposed in this pull request?
With doc to say this would convert DF into RDD
## How was this patch tested?
unit tests, manual tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16668 from felixcheung/rgetnumpartitions.
## What changes were proposed in this pull request?
Add R wrapper for bisecting Kmeans.
As JIRA is down, I will update title to link with corresponding JIRA later.
## How was this patch tested?
Add new unit tests.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16566 from wangmiao1981/bk.
## What changes were proposed in this pull request?
Support for
```
df[[myname]] <- 1
df[[2]] <- df$eruptions
```
## How was this patch tested?
manual tests, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16663 from felixcheung/rcolset.
## What changes were proposed in this pull request?
```spark.gaussianMixture``` supports output total log-likelihood for the model like R ```mvnormalmixEM```.
## How was this patch tested?
R unit test.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16646 from yanboliang/spark-19291.
## What changes were proposed in this pull request?
When R is starting as a package and it needs to download the Spark release distribution we need to handle error for download and untar, and clean up, otherwise it will get stuck.
## How was this patch tested?
manually
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16589 from felixcheung/rtarreturncode.
## What changes were proposed in this pull request?
Refactored script to remove duplications and clearer purpose for each script
## How was this patch tested?
manually
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16249 from felixcheung/rscripts.
## What changes were proposed in this pull request?
Windows seems to be the only place with appauthor in the path, for which we should say "Apache" (and case sensitive)
Current path of `AppData\Local\spark\spark\Cache` is a bit odd.
## How was this patch tested?
manual.
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16590 from felixcheung/rcachedir.
## What changes were proposed in this pull request?
spark.lda passes the optimizer "em" or "online" as a string to the backend. However, LDAWrapper doesn't set optimizer based on the value from R. Therefore, for optimizer "em", the `isDistributed` field is FALSE, which should be TRUE based on scala code.
In addition, the `summary` method should bring back the results related to `DistributedLDAModel`.
## How was this patch tested?
Manual tests by comparing with scala example.
Modified the current unit test: fix the incorrect unit test and add necessary tests for `summary` method.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16464 from wangmiao1981/new.
## What changes were proposed in this pull request?
To allow specifying number of partitions when the DataFrame is created
## How was this patch tested?
manual, unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16512 from felixcheung/rnumpart.
## What changes were proposed in this pull request?
spark.kmeans doesn't have interface to set initSteps, seed and tol. As Spark Kmeans algorithm doesn't take the same set of parameters as R kmeans, we should maintain a different interface in spark.kmeans.
Add missing parameters and corresponding document.
Modified existing unit tests to take additional parameters.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16523 from wangmiao1981/kmeans.
## What changes were proposed in this pull request?
```
df$foo <- 1
```
instead of
```
df$foo <- lit(1)
```
## How was this patch tested?
unit tests
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16510 from felixcheung/rlitcol.
## What changes were proposed in this pull request?
R family is a longer list than what Spark supports.
## How was this patch tested?
manual
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16511 from felixcheung/rdocglmfamily.
## What changes were proposed in this pull request?
- [X] Make sure all join types are clearly mentioned
- [X] Make join labeling/style consistent
- [X] Make join label ordering docs the same
- [X] Improve join documentation according to above for Scala
- [X] Improve join documentation according to above for Python
- [X] Improve join documentation according to above for R
## How was this patch tested?
No tests b/c docs.
Please review http://spark.apache.org/contributing.html before opening a pull request.
Author: anabranch <wac.chambers@gmail.com>
Closes#16504 from anabranch/SPARK-19126.
## What changes were proposed in this pull request?
- [X] Fix inconsistencies in function reference for dense rank and dense
- [X] Make all languages equivalent in their reference to `dense_rank` and `rank`.
## How was this patch tested?
N/A for docs.
Please review http://spark.apache.org/contributing.html before opening a pull request.
Author: anabranch <wac.chambers@gmail.com>
Closes#16505 from anabranch/SPARK-19127.
## What changes were proposed in this pull request?
SparkR ```mllib.R``` is getting bigger as we add more ML wrappers, I'd like to split it into multiple files to make us easy to maintain:
* mllib_classification.R
* mllib_clustering.R
* mllib_recommendation.R
* mllib_regression.R
* mllib_stat.R
* mllib_tree.R
* mllib_utils.R
Note: Only reorg, no actual code change.
## How was this patch tested?
Existing tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16312 from yanboliang/spark-18862.
## What changes were proposed in this pull request?
#16126 bumps master branch version to 2.2.0-SNAPSHOT, but it seems R version was omitted.
## How was this patch tested?
N/A
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16488 from yanboliang/r-version.
## 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?
SparkR tests, `R/run-tests.sh`, succeeds only once because `test_sparkSQL.R` does not clean up the test table, `people`.
As a result, the rows in `people` table are accumulated at every run and the test cases fail.
The following is the failure result for the second run.
```r
Failed -------------------------------------------------------------------------
1. Failure: create DataFrame from RDD (test_sparkSQL.R#204) -------------------
collect(sql("SELECT age from people WHERE name = 'Bob'"))$age not equal to c(16).
Lengths differ: 2 vs 1
2. Failure: create DataFrame from RDD (test_sparkSQL.R#206) -------------------
collect(sql("SELECT height from people WHERE name ='Bob'"))$height not equal to c(176.5).
Lengths differ: 2 vs 1
```
## How was this patch tested?
Manual. Run `run-tests.sh` twice and check if it passes without failures.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#16310 from dongjoon-hyun/SPARK-18897.
## What changes were proposed in this pull request?
doc cleanup
## How was this patch tested?
~~vignettes is not building for me. I'm going to kick off a full clean build and try again and attach output here for review.~~
Output html here: https://felixcheung.github.io/sparkr-vignettes.html
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16286 from felixcheung/rvignettespass.
## What changes were proposed in this pull request?
When do the QA work, I found that the following issues:
1). `spark.mlp` doesn't include an example;
2). `spark.mlp` and `spark.lda` have redundant parameter explanations;
3). `spark.lda` document misses default values for some parameters.
I also changed the `spark.logit` regParam in the examples, as we discussed in #16222.
## How was this patch tested?
Manual test
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16284 from wangmiao1981/ks.
## What changes were proposed in this pull request?
Added short section for KSTest.
Also added logreg model to list of ML models in vignette. (This will be reorganized under SPARK-18849)
![screen shot 2016-12-14 at 1 37 31 pm](https://cloud.githubusercontent.com/assets/5084283/21202140/7f24e240-c202-11e6-9362-458208bb9159.png)
## How was this patch tested?
Manually tested example locally.
Built vignettes locally.
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#16283 from jkbradley/ksTest-vignette.
## What changes were proposed in this pull request?
While adding vignettes for kstest, I found some errors in the example:
1. There is a typo of kstest;
2. print.summary.KStest doesn't work with the example;
Fix the example errors;
Add a new unit test for print.summary.KStest;
## How was this patch tested?
Manual test;
Add new unit test;
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16259 from wangmiao1981/ks.
## What changes were proposed in this pull request?
Mention `spark.randomForest` and `spark.gbt` in vignettes. Keep the content minimal since users can type `?spark.randomForest` to see the full doc.
cc: jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Closes#16264 from mengxr/SPARK-18793.
## What changes were proposed in this pull request?
Support overriding the download url (include version directory) in an environment variable, `SPARKR_RELEASE_DOWNLOAD_URL`
## How was this patch tested?
unit test, manually testing
- snapshot build url
- download when spark jar not cached
- when spark jar is cached
- RC build url
- download when spark jar not cached
- when spark jar is cached
- multiple cached spark versions
- starting with sparkR shell
To use this,
```
SPARKR_RELEASE_DOWNLOAD_URL=http://this_is_the_url_to_spark_release_tgz R
```
then in R,
```
library(SparkR) # or specify lib.loc
sparkR.session()
```
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16248 from felixcheung/rinstallurl.
## What changes were proposed in this pull request?
Several SparkR API calling into JVM methods that have void return values are getting printed out, especially when running in a REPL or IDE.
example:
```
> setLogLevel("WARN")
NULL
```
We should fix this to make the result more clear.
Also found a small change to return value of dropTempView in 2.1 - adding doc and test for it.
## How was this patch tested?
manually - I didn't find a expect_*() method in testthat for this
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16237 from felixcheung/rinvis.
## What changes were proposed in this pull request?
In this PR, the document of `summary` method is improved in the format:
returns summary information of the fitted model, which is a list. The list includes .......
Since `summary` in R is mainly about the model, which is not the same as `summary` object on scala side, if there is one, the scala API doc is not pointed here.
In current document, some `return` have `.` and some don't have. `.` is added to missed ones.
Since spark.logit `summary` has a big refactoring, this PR doesn't include this one. It will be changed when the `spark.logit` PR is merged.
## How was this patch tested?
Manual build.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#16150 from wangmiao1981/audit2.
## 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?
Reviewing SparkR ML wrappers API for 2.1 release, mainly two issues:
* Remove ```probabilityCol``` from the argument list of ```spark.logit``` and ```spark.randomForest```. Since it was used when making prediction and should be an argument of ```predict```, and we will work on this at [SPARK-18618](https://issues.apache.org/jira/browse/SPARK-18618) in the next release cycle.
* Fix ```spark.als``` params to make it consistent with MLlib.
## How was this patch tested?
Existing tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16169 from yanboliang/spark-18326.
## What changes were proposed in this pull request?
Fix reservoir sampling bias for small k. An off-by-one error meant that the probability of replacement was slightly too high -- k/(l-1) after l element instead of k/l, which matters for small k.
## How was this patch tested?
Existing test plus new test case.
Author: Sean Owen <sowen@cloudera.com>
Closes#16129 from srowen/SPARK-18678.
## What changes were proposed in this pull request?
Several cleanup and improvements for ```spark.logit```:
* ```summary``` should return coefficients matrix, and should output labels for each class if the model is multinomial logistic regression model.
* ```summary``` should not return ```areaUnderROC, roc, pr, ...```, since most of them are DataFrame which are less important for R users. Meanwhile, these metrics ignore instance weights (setting all to 1.0) which will be changed in later Spark version. In case it will introduce breaking changes, we do not expose them currently.
* SparkR test improvement: comparing the training result with native R glmnet.
* Remove argument ```aggregationDepth``` from ```spark.logit```, since it's an expert Param(related with Spark architecture and job execution) that would be used rarely by R users.
## How was this patch tested?
Unit tests.
The ```summary``` output after this change:
multinomial logistic regression:
```
> df <- suppressWarnings(createDataFrame(iris))
> model <- spark.logit(df, Species ~ ., regParam = 0.5)
> summary(model)
$coefficients
versicolor virginica setosa
(Intercept) 1.514031 -2.609108 1.095077
Sepal_Length 0.02511006 0.2649821 -0.2900921
Sepal_Width -0.5291215 -0.02016446 0.549286
Petal_Length 0.03647411 0.1544119 -0.190886
Petal_Width 0.000236092 0.4195804 -0.4198165
```
binomial logistic regression:
```
> df <- suppressWarnings(createDataFrame(iris))
> training <- df[df$Species %in% c("versicolor", "virginica"), ]
> model <- spark.logit(training, Species ~ ., regParam = 0.5)
> summary(model)
$coefficients
Estimate
(Intercept) -6.053815
Sepal_Length 0.2449379
Sepal_Width 0.1648321
Petal_Length 0.4730718
Petal_Width 1.031947
```
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16117 from yanboliang/spark-18686.
## What changes were proposed in this pull request?
If SparkR is running as a package and it has previously downloaded Spark Jar it should be able to run as before without having to set SPARK_HOME. Basically with this bug the auto install Spark will only work in the first session.
This seems to be a regression on the earlier behavior.
Fix is to always try to install or check for the cached Spark if running in an interactive session.
As discussed before, we should probably only install Spark iff running in an interactive session (R shell, RStudio etc)
## How was this patch tested?
Manually
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#16077 from felixcheung/rsessioninteractive.
## What changes were proposed in this pull request?
It's better we can fix this issue by providing an option ```type``` for users to change the ```predict``` output schema, then they could output probabilities, log-space predictions, or original labels. In order to not involve breaking API change for 2.1, so revert this change firstly and will add it back after [SPARK-18618](https://issues.apache.org/jira/browse/SPARK-18618) resolved.
## How was this patch tested?
Existing unit tests.
This reverts commit daa975f4bf.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#16118 from yanboliang/spark-18291-revert.