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* [SPARK-16446][SPARKR][ML] Gaussian Mixture Model wrapper in SparkRYanbo Liang2016-08-174-3/+208
| | | | | | | | | | | | ## 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.
* [SPARK-16444][SPARKR] Isotonic Regression wrapper in SparkRwm624@hotmail.com2016-08-174-1/+156
| | | | | | | | | | | | | | | | | | | | | ## 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.
* [SPARK-16519][SPARKR] Handle SparkR RDD generics that create warnings in R ↵Felix Cheung2016-08-1617-287/+312
| | | | | | | | | | | | | | | | | CMD check ## What changes were proposed in this pull request? Rename RDD functions for now to avoid CRAN check warnings. Some RDD functions are sharing generics with DataFrame functions (hence the problem) so after the renames we need to add new generics, for now. ## How was this patch tested? unit tests Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14626 from felixcheung/rrddfunctions.
* [MINOR][SPARKR] spark.glm weightCol should in the signature.Yanbo Liang2016-08-161-1/+1
| | | | | | | | | | | | ## What changes were proposed in this pull request? Fix the issue that ```spark.glm``` ```weightCol``` should in the signature. ## How was this patch tested? Existing tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #14641 from yanboliang/weightCol.
* [SPARK-16508][SPARKR] Split docs for arrange and orderBy methodsJunyang Qian2016-08-153-15/+16
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR splits arrange and orderBy methods according to their functionality (the former for sorting sparkDataFrame and the latter for windowSpec). ## How was this patch tested? ![screen shot 2016-08-06 at 6 39 19 pm](https://cloud.githubusercontent.com/assets/15318264/17459969/51eade28-5c05-11e6-8ca1-8d8a8e344bab.png) ![screen shot 2016-08-06 at 6 39 29 pm](https://cloud.githubusercontent.com/assets/15318264/17459966/51e3c246-5c05-11e6-8d35-3e905ca48676.png) ![screen shot 2016-08-06 at 6 40 02 pm](https://cloud.githubusercontent.com/assets/15318264/17459967/51e650ec-5c05-11e6-8698-0f037f5199ff.png) Author: Junyang Qian <junyangq@databricks.com> Closes #14522 from junyangq/SPARK-16508-0.
* [SPARK-16579][SPARKR] add install.spark functionJunyang Qian2016-08-107-4/+267
| | | | | | | | | | | | | | | | | | | | | | | | | | ## 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.
* [SPARK-16710][SPARKR][ML] spark.glm should support weightColYanbo Liang2016-08-102-4/+33
| | | | | | | | | | | | ## What changes were proposed in this pull request? Training GLMs on weighted dataset is very important use cases, but it is not supported by SparkR currently. Users can pass argument ```weights``` to specify the weights vector in native R. For ```spark.glm```, we can pass in the ```weightCol``` which is consistent with MLlib. ## How was this patch tested? Unit test. Author: Yanbo Liang <ybliang8@gmail.com> Closes #14346 from yanboliang/spark-16710.
* [MINOR][SPARKR] R API documentation for "coltypes" is confusingXin Ren2016-08-101-5/+4
| | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? R API documentation for "coltypes" is confusing, found when working on another ticket. Current version http://spark.apache.org/docs/2.0.0/api/R/coltypes.html, where parameters have 2 "x" which is a duplicate, and also the example is not very clear ![current](https://cloud.githubusercontent.com/assets/3925641/17386808/effb98ce-59a2-11e6-9657-d477d258a80c.png) ![screen shot 2016-08-03 at 5 56 00 pm](https://cloud.githubusercontent.com/assets/3925641/17386884/91831096-59a3-11e6-84af-39890b3d45d8.png) ## How was this patch tested? Tested manually on local machine. And the screenshots are like below: ![screen shot 2016-08-07 at 11 29 20 pm](https://cloud.githubusercontent.com/assets/3925641/17471144/df36633c-5cf6-11e6-8238-4e32ead0e529.png) ![screen shot 2016-08-03 at 5 56 22 pm](https://cloud.githubusercontent.com/assets/3925641/17386896/9d36cb26-59a3-11e6-9619-6dae29f7ab17.png) Author: Xin Ren <iamshrek@126.com> Closes #14489 from keypointt/rExample.
* [SPARKR][DOCS] fix broken url in docFelix Cheung2016-07-252-9/+9
| | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Fix broken url, also, sparkR.session.stop doc page should have it in the header, instead of saying "sparkR.stop" ![image](https://cloud.githubusercontent.com/assets/8969467/17080129/26d41308-50d9-11e6-8967-79d6c920313f.png) Data type section is in the middle of a list of gapply/gapplyCollect subsections: ![image](https://cloud.githubusercontent.com/assets/8969467/17080122/f992d00a-50d8-11e6-8f2c-fd5786213920.png) ## How was this patch tested? manual test Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14329 from felixcheung/rdoclinkfix.
* [SPARK-10683][SPARK-16510][SPARKR] Move SparkR include jar test to ↵Shivaram Venkataraman2016-07-193-41/+5
| | | | | | | | | | | | | | | SparkSubmitSuite ## What changes were proposed in this pull request? This change moves the include jar test from R to SparkSubmitSuite and uses a dynamically compiled jar. This helps us remove the binary jar from the R package and solves both the CRAN warnings and the lack of source being available for this jar. ## How was this patch tested? SparkR unit tests, SparkSubmitSuite, check-cran.sh Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #14243 from shivaram/sparkr-jar-move.
* [SPARK-16055][SPARKR] warning added while using sparkPackages with spark-submitkrishnakalyan32016-07-181-0/+4
| | | | | | | | | | | | | ## What changes were proposed in this pull request? https://issues.apache.org/jira/browse/SPARK-16055 sparkPackages - argument is passed and we detect that we are in the R script mode, we should print some warning like --packages flag should be used with with spark-submit ## How was this patch tested? In my system locally Author: krishnakalyan3 <krishnakalyan3@gmail.com> Closes #14179 from krishnakalyan3/spark-pkg.
* [SPARK-16027][SPARKR] Fix R tests SparkSession init/stopFelix Cheung2016-07-1714-25/+48
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Fix R SparkSession init/stop, and warnings of reusing existing Spark Context ## How was this patch tested? unit tests shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14177 from felixcheung/rsessiontest.
* [SPARK-16507][SPARKR] Add a CRAN checker, fix Rd aliasesShivaram Venkataraman2016-07-1616-43/+675
| | | | | | | | | | | | | | | | | | ## 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.
* [SPARK-16538][SPARKR] Add more tests for namespace call to SparkSession ↵Felix Cheung2016-07-151-0/+7
| | | | | | | | | | | | | | | | | | | functions ## What changes were proposed in this pull request? More tests I don't think this is critical for Spark 2.0.0 RC, maybe Spark 2.0.1 or 2.1.0. ## How was this patch tested? unit tests shivaram dongjoon-hyun Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14206 from felixcheung/rroutetests.
* [SPARK-16538][SPARKR] fix R call with namespace operator on SparkSession ↵Felix Cheung2016-07-142-2/+5
| | | | | | | | | | | | | | | | | | functions ## What changes were proposed in this pull request? Fix function routing to work with and without namespace operator `SparkR::createDataFrame` ## How was this patch tested? manual, unit tests shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14195 from felixcheung/rroutedefault.
* [SPARK-16509][SPARKR] Rename window.partitionBy and window.orderBy to ↵Sun Rui2016-07-145-34/+44
| | | | | | | | | | | | | | windowPartitionBy and windowOrderBy. ## 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.
* [SPARKR][DOCS][MINOR] R programming guide to include csv data source exampleFelix Cheung2016-07-131-1/+1
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Minor documentation update for code example, code style, and missed reference to "sparkR.init" ## How was this patch tested? manual shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14178 from felixcheung/rcsvprogrammingguide.
* [SPARKR][MINOR] R examples and test updatesFelix Cheung2016-07-132-2/+2
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Minor example updates ## How was this patch tested? manual shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14171 from felixcheung/rexample.
* [SPARK-16144][SPARKR] update R API doc for mllibFelix Cheung2016-07-112-8/+30
| | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? From SPARK-16140/PR #13921 - the issue is we left write.ml doc empty: ![image](https://cloud.githubusercontent.com/assets/8969467/16481934/856dd0ea-3e62-11e6-9474-e4d57d1ca001.png) Here's what I meant as the fix: ![image](https://cloud.githubusercontent.com/assets/8969467/16481943/911f02ec-3e62-11e6-9d68-17363a9f5628.png) ![image](https://cloud.githubusercontent.com/assets/8969467/16481950/9bc057aa-3e62-11e6-8127-54870701c4b1.png) I didn't realize there was already a JIRA on this. mengxr yanboliang ## How was this patch tested? check doc generated. Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13993 from felixcheung/rmllibdoc.
* [SPARKR][DOC] SparkR ML user guides update for 2.0Yanbo Liang2016-07-111-3/+5
| | | | | | | | | | | | | ## What changes were proposed in this pull request? * Update SparkR ML section to make them consistent with SparkR API docs. * Since #13972 adds labelling support for the ```include_example``` Jekyll plugin, so that we can split the single ```ml.R``` example file into multiple line blocks with different labels, and include them in different algorithms/models in the generated HTML page. ## How was this patch tested? Only docs update, manually check the generated docs. Author: Yanbo Liang <ybliang8@gmail.com> Closes #14011 from yanboliang/r-user-guide-update.
* [SPARK-16429][SQL] Include `StringType` columns in `describe()`Dongjoon Hyun2016-07-082-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Currently, Spark `describe` supports `StringType`. However, `describe()` returns a dataset for only all numeric columns. This PR aims to include `StringType` columns in `describe()`, `describe` without argument. **Background** ```scala scala> spark.read.json("examples/src/main/resources/people.json").describe("age", "name").show() +-------+------------------+-------+ |summary| age| name| +-------+------------------+-------+ | count| 2| 3| | mean| 24.5| null| | stddev|7.7781745930520225| null| | min| 19| Andy| | max| 30|Michael| +-------+------------------+-------+ ``` **Before** ```scala scala> spark.read.json("examples/src/main/resources/people.json").describe().show() +-------+------------------+ |summary| age| +-------+------------------+ | count| 2| | mean| 24.5| | stddev|7.7781745930520225| | min| 19| | max| 30| +-------+------------------+ ``` **After** ```scala scala> spark.read.json("examples/src/main/resources/people.json").describe().show() +-------+------------------+-------+ |summary| age| name| +-------+------------------+-------+ | count| 2| 3| | mean| 24.5| null| | stddev|7.7781745930520225| null| | min| 19| Andy| | max| 30|Michael| +-------+------------------+-------+ ``` ## How was this patch tested? Pass the Jenkins with a update testcase. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #14095 from dongjoon-hyun/SPARK-16429.
* [SPARK-16425][R] `describe()` should not fail with non-numeric columnsDongjoon Hyun2016-07-072-4/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR prevents ERRORs when `summary(df)` is called for `SparkDataFrame` with not-numeric columns. This failure happens only in `SparkR`. **Before** ```r > df <- createDataFrame(faithful) > df <- withColumn(df, "boolean", df$waiting==79) > summary(df) 16/07/07 14:15:16 ERROR RBackendHandler: describe on 34 failed Error in invokeJava(isStatic = FALSE, objId$id, methodName, ...) : org.apache.spark.sql.AnalysisException: cannot resolve 'avg(`boolean`)' due to data type mismatch: function average requires numeric types, not BooleanType; ``` **After** ```r > df <- createDataFrame(faithful) > df <- withColumn(df, "boolean", df$waiting==79) > summary(df) SparkDataFrame[summary:string, eruptions:string, waiting:string] ``` ## How was this patch tested? Pass the Jenkins with a updated testcase. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #14096 from dongjoon-hyun/SPARK-16425.
* [SPARK-16310][SPARKR] R na.string-like default for csv sourceFelix Cheung2016-07-072-8/+34
| | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Apply default "NA" as null string for R, like R read.csv na.string parameter. https://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html na.strings = "NA" An user passing a csv file with NA value should get the same behavior with SparkR read.df(... source = "csv") (couldn't open JIRA, will do that later) ## How was this patch tested? unit tests shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13984 from felixcheung/rcsvnastring.
* [SPARK-16233][R][TEST] ORC test should be enabled only when HiveContext is ↵Dongjoon Hyun2016-07-011-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | available. ## What changes were proposed in this pull request? ORC test should be enabled only when HiveContext is available. ## How was this patch tested? Manual. ``` $ R/run-tests.sh ... 1. create DataFrame from RDD (test_sparkSQL.R#200) - Hive is not build with SparkSQL, skipped 2. test HiveContext (test_sparkSQL.R#1021) - Hive is not build with SparkSQL, skipped 3. read/write ORC files (test_sparkSQL.R#1728) - Hive is not build with SparkSQL, skipped 4. enableHiveSupport on SparkSession (test_sparkSQL.R#2448) - Hive is not build with SparkSQL, skipped 5. sparkJars tag in SparkContext (test_Windows.R#21) - This test is only for Windows, skipped DONE =========================================================================== Tests passed. ``` Author: Dongjoon Hyun <dongjoon@apache.org> Closes #14019 from dongjoon-hyun/SPARK-16233.
* [SPARK-16299][SPARKR] Capture errors from R workers in daemon.R to avoid ↵Sun Rui2016-07-011-1/+1
| | | | | | | | | | | | | | deletion of R session temporary directory. ## What changes were proposed in this pull request? Capture errors from R workers in daemon.R to avoid deletion of R session temporary directory. See detailed description at https://issues.apache.org/jira/browse/SPARK-16299 ## How was this patch tested? SparkR unit tests. Author: Sun Rui <sunrui2016@gmail.com> Closes #13975 from sun-rui/SPARK-16299.
* [SPARK-16012][SPARKR] Implement gapplyCollect which will apply a R function ↵Narine Kokhlikyan2016-07-015-67/+177
| | | | | | | | | | | | | | | | on each group similar to gapply and collect the result back to R data.frame ## 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.
* [SPARK-16289][SQL] Implement posexplode table generating functionDongjoon Hyun2016-06-304-1/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## 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.
* [SPARK-16140][MLLIB][SPARKR][DOCS] Group k-means method in generated R docXin Ren2016-06-292-39/+35
| | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-16140 ## What changes were proposed in this pull request? Group the R doc of spark.kmeans, predict(KM), summary(KM), read/write.ml(KM) under Rd spark.kmeans. The example code was updated. ## How was this patch tested? Tested on my local machine And on my laptop `jekyll build` is failing to build API docs, so here I can only show you the html I manually generated from Rd files, with no CSS applied, but the doc content should be there. ![screenshotkmeans](https://cloud.githubusercontent.com/assets/3925641/16403203/c2c9ca1e-3ca7-11e6-9e29-f2164aee75fc.png) Author: Xin Ren <iamshrek@126.com> Closes #13921 from keypointt/SPARK-16140.
* [MINOR][SPARKR] Fix arguments of survreg in SparkRYanbo Liang2016-06-291-2/+2
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Fix wrong arguments description of ```survreg``` in SparkR. ## How was this patch tested? ```Arguments``` section of ```survreg``` doc before this PR (with wrong description for ```path``` and missing ```overwrite```): ![image](https://cloud.githubusercontent.com/assets/1962026/16447548/fe7a5ed4-3da1-11e6-8b96-b5bf2083b07e.png) After this PR: ![image](https://cloud.githubusercontent.com/assets/1962026/16447617/368e0b18-3da2-11e6-8277-45640fb11859.png) Author: Yanbo Liang <ybliang8@gmail.com> Closes #13970 from yanboliang/spark-16143-followup.
* [SPARKR] add csv testsFelix Cheung2016-06-281-0/+18
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Add unit tests for csv data for SPARKR ## How was this patch tested? unit tests Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13904 from felixcheung/rcsv.
* [MINOR][SPARKR] update sparkR DataFrame.R commentWeichenXu2016-06-281-2/+2
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? update sparkR DataFrame.R comment SQLContext ==> SparkSession ## How was this patch tested? N/A Author: WeichenXu <WeichenXu123@outlook.com> Closes #13946 from WeichenXu123/sparkR_comment_update_sparkSession.
* [SPARK-16128][SQL] Allow setting length of characters to be truncated to, in ↵Prashant Sharma2016-06-282-3/+16
| | | | | | | | | | | | | | | | | | Dataset.show function. ## What changes were proposed in this pull request? Allowing truncate to a specific number of character is convenient at times, especially while operating from the REPL. Sometimes those last few characters make all the difference, and showing everything brings in whole lot of noise. ## How was this patch tested? Existing tests. + 1 new test in DataFrameSuite. For SparkR and pyspark, existing tests and manual testing. Author: Prashant Sharma <prashsh1@in.ibm.com> Author: Prashant Sharma <prashant@apache.org> Closes #13839 from ScrapCodes/add_truncateTo_DF.show.
* [SPARK-16143][R] group AFT survival regression methods docs in a single RdJunyang Qian2016-06-271-46/+42
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR groups `spark.survreg`, `summary(AFT)`, `predict(AFT)`, `write.ml(AFT)` for survival regression into a single Rd. ## How was this patch tested? Manually checked generated HTML doc. See attached screenshots. ![screen shot 2016-06-27 at 10 28 20 am](https://cloud.githubusercontent.com/assets/15318264/16392008/a14cf472-3c5e-11e6-9ce5-490ed1a52249.png) ![screen shot 2016-06-27 at 10 28 35 am](https://cloud.githubusercontent.com/assets/15318264/16392009/a14e333c-3c5e-11e6-8bd7-c2e9ba71f8e2.png) Author: Junyang Qian <junyangq@databricks.com> Closes #13927 from junyangq/SPARK-16143.
* [SPARK-16184][SPARKR] conf API for SparkSessionFelix Cheung2016-06-263-10/+53
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## 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.
* [SPARK-16142][R] group naiveBayes method docs in a single RdXiangrui Meng2016-06-231-48/+42
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR groups `spark.naiveBayes`, `summary(NB)`, `predict(NB)`, and `write.ml(NB)` into a single Rd. ## How was this patch tested? Manually checked generated HTML doc. See attached screenshots. ![screen shot 2016-06-23 at 2 11 00 pm](https://cloud.githubusercontent.com/assets/829644/16320452/a5885e92-394c-11e6-994f-2ab5cddad86f.png) ![screen shot 2016-06-23 at 2 11 15 pm](https://cloud.githubusercontent.com/assets/829644/16320455/aad1f6d8-394c-11e6-8ef4-13bee989f52f.png) Author: Xiangrui Meng <meng@databricks.com> Closes #13877 from mengxr/SPARK-16142.
* [SPARK-16088][SPARKR] update setJobGroup, cancelJobGroup, clearJobGroupFelix Cheung2016-06-235-24/+73
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Updated setJobGroup, cancelJobGroup, clearJobGroup to not require sc/SparkContext as parameter. Also updated roxygen2 doc and R programming guide on deprecations. ## How was this patch tested? unit tests Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13838 from felixcheung/rjobgroup.
* [SPARK-15672][R][DOC] R programming guide updateKai Jiang2016-06-221-1/+1
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Guide for - UDFs with dapply, dapplyCollect - spark.lapply for running parallel R functions ## How was this patch tested? build locally <img width="654" alt="screen shot 2016-06-14 at 03 12 56" src="https://cloud.githubusercontent.com/assets/3419881/16039344/12a3b6a0-31de-11e6-8d77-fe23308075c0.png"> Author: Kai Jiang <jiangkai@gmail.com> Closes #13660 from vectorijk/spark-15672-R-guide-update.
* [SPARK-16107][R] group glm methods in documentationJunyang Qian2016-06-221-44/+36
| | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This groups GLM methods (spark.glm, summary, print, predict and write.ml) in the documentation. The example code was updated. ## How was this patch tested? N/A (If this patch involves UI changes, please attach a screenshot; otherwise, remove this) ![screen shot 2016-06-21 at 2 31 37 pm](https://cloud.githubusercontent.com/assets/15318264/16247077/f6eafc04-37bc-11e6-89a8-7898ff3e4078.png) ![screen shot 2016-06-21 at 2 31 45 pm](https://cloud.githubusercontent.com/assets/15318264/16247078/f6eb1c16-37bc-11e6-940a-2b595b10617c.png) Author: Junyang Qian <junyangq@databricks.com> Author: Junyang Qian <junyangq@Junyangs-MacBook-Pro.local> Closes #13820 from junyangq/SPARK-16107.
* [SPARK-16096][SPARKR] add union and deprecate unionAllFelix Cheung2016-06-215-13/+47
| | | | | | | | | | | | | | | | ## 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.
* [SPARK-16109][SPARKR][DOC] R more doc fixesFelix Cheung2016-06-215-23/+40
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Found these issues while reviewing for SPARK-16090 ## How was this patch tested? roxygen2 doc gen, checked output html Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13803 from felixcheung/rdocrd.
* [SPARK-15177][.1][R] make SparkR model params and default values consistent ↵Xiangrui Meng2016-06-212-40/+38
| | | | | | | | | | | | | | | | | | | | | with MLlib ## What changes were proposed in this pull request? This PR is a subset of #13023 by yanboliang to make SparkR model param names and default values consistent with MLlib. I tried to avoid other changes from #13023 to keep this PR minimal. I will send a follow-up PR to improve the documentation. Main changes: * `spark.glm`: epsilon -> tol, maxit -> maxIter * `spark.kmeans`: default k -> 2, default maxIter -> 20, default initMode -> "k-means||" * `spark.naiveBayes`: laplace -> smoothing, default 1.0 ## How was this patch tested? Existing unit tests. Author: Xiangrui Meng <meng@databricks.com> Closes #13801 from mengxr/SPARK-15177.1.
* [SPARK-15319][SPARKR][DOCS] Fix SparkR doc layout for corr and other ↵Felix Cheung2016-06-212-23/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | DataFrame stats functions ## What changes were proposed in this pull request? Doc only changes. Please see screenshots. Before: http://spark.apache.org/docs/latest/api/R/statfunctions.html ![image](https://cloud.githubusercontent.com/assets/8969467/15264110/cd458826-1924-11e6-85bd-8ee2e2e1a85f.png) After ![image](https://cloud.githubusercontent.com/assets/8969467/16218452/b9e89f08-3732-11e6-969d-a3a1796e7ad0.png) (please ignore the style differences - this is due to not having the css in my local copy) This is still a bit weird. As discussed in SPARK-15237, I think the better approach is to separate out the DataFrame stats function instead of putting everything on one page. At least now it is clearer which description is on which function. ## How was this patch tested? Build doc Author: Felix Cheung <felixcheung_m@hotmail.com> Author: felixcheung <felixcheung_m@hotmail.com> Closes #13109 from felixcheung/rstatdoc.
* [SPARKR][DOCS] R code doc cleanupFelix Cheung2016-06-208-84/+70
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? I ran a full pass from A to Z and fixed the obvious duplications, improper grouping etc. There are still more doc issues to be cleaned up. ## How was this patch tested? manual tests Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13798 from felixcheung/rdocseealso.
* [SPARK-15294][R] Add `pivot` to SparkRDongjoon Hyun2016-06-204-0/+73
| | | | | | | | | | | | | | ## 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.
* remove duplicated docs in dapplyNarine Kokhlikyan2016-06-202-2/+4
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Removed unnecessary duplicated documentation in dapply and dapplyCollect. In this pull request I created separate R docs for dapply and dapplyCollect - kept dapply's documentation separate from dapplyCollect's and referred from one to another via a link. ## How was this patch tested? Existing test cases. Author: Narine Kokhlikyan <narine@slice.com> Closes #13790 from NarineK/dapply-docs-fix.
* [SPARK-14995][R] Add `since` tag in Roxygen documentation for SparkR API methodsDongjoon Hyun2016-06-2014-34/+340
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR adds `since` tags to Roxygen documentation according to the previous documentation archive. https://home.apache.org/~dongjoon/spark-2.0.0-docs/api/R/ ## How was this patch tested? Manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #13734 from dongjoon-hyun/SPARK-14995.
* [SPARK-15159][SPARKR] SparkSession roxygen2 doc, programming guide, example ↵Felix Cheung2016-06-205-161/+92
| | | | | | | | | | | | | | | | | updates ## What changes were proposed in this pull request? roxygen2 doc, programming guide, example updates ## How was this patch tested? manual checks shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13751 from felixcheung/rsparksessiondoc.
* [SPARK-16053][R] Add `spark_partition_id` in SparkRDongjoon Hyun2016-06-204-0/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## 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.
* [SPARKR] fix R roxygen2 doc for count on GroupedDataFelix Cheung2016-06-201-1/+3
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? fix code doc ## How was this patch tested? manual shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13782 from felixcheung/rcountdoc.
* [SPARK-16028][SPARKR] spark.lapply can work with active contextFelix Cheung2016-06-202-10/+16
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? spark.lapply and setLogLevel ## How was this patch tested? unit test shivaram thunterdb Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13752 from felixcheung/rlapply.
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