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* [SPARK-17210][SPARKR] sparkr.zip is not distributed to executors when ↵Jeff Zhang2016-09-231-0/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | running sparkr in RStudio ## What changes were proposed in this pull request? Spark will add sparkr.zip to archive only when it is yarn mode (SparkSubmit.scala). ``` if (args.isR && clusterManager == YARN) { val sparkRPackagePath = RUtils.localSparkRPackagePath if (sparkRPackagePath.isEmpty) { printErrorAndExit("SPARK_HOME does not exist for R application in YARN mode.") } val sparkRPackageFile = new File(sparkRPackagePath.get, SPARKR_PACKAGE_ARCHIVE) if (!sparkRPackageFile.exists()) { printErrorAndExit(s"$SPARKR_PACKAGE_ARCHIVE does not exist for R application in YARN mode.") } val sparkRPackageURI = Utils.resolveURI(sparkRPackageFile.getAbsolutePath).toString // Distribute the SparkR package. // Assigns a symbol link name "sparkr" to the shipped package. args.archives = mergeFileLists(args.archives, sparkRPackageURI + "#sparkr") // Distribute the R package archive containing all the built R packages. if (!RUtils.rPackages.isEmpty) { val rPackageFile = RPackageUtils.zipRLibraries(new File(RUtils.rPackages.get), R_PACKAGE_ARCHIVE) if (!rPackageFile.exists()) { printErrorAndExit("Failed to zip all the built R packages.") } val rPackageURI = Utils.resolveURI(rPackageFile.getAbsolutePath).toString // Assigns a symbol link name "rpkg" to the shipped package. args.archives = mergeFileLists(args.archives, rPackageURI + "#rpkg") } } ``` So it is necessary to pass spark.master from R process to JVM. Otherwise sparkr.zip won't be distributed to executor. Besides that I also pass spark.yarn.keytab/spark.yarn.principal to spark side, because JVM process need them to access secured cluster. ## How was this patch tested? Verify it manually in R Studio using the following code. ``` Sys.setenv(SPARK_HOME="/Users/jzhang/github/spark") .libPaths(c(file.path(Sys.getenv(), "R", "lib"), .libPaths())) library(SparkR) sparkR.session(master="yarn-client", sparkConfig = list(spark.executor.instances="1")) df <- as.DataFrame(mtcars) head(df) ``` … Author: Jeff Zhang <zjffdu@apache.org> Closes #14784 from zjffdu/SPARK-17210.
* [SPARK-17445][DOCS] Reference an ASF page as the main place to find ↵Sean Owen2016-09-141-1/+2
| | | | | | | | | | | | | | | | | | third-party packages ## What changes were proposed in this pull request? Point references to spark-packages.org to https://cwiki.apache.org/confluence/display/SPARK/Third+Party+Projects This will be accompanied by a parallel change to the spark-website repo, and additional changes to this wiki. ## How was this patch tested? Jenkins tests. Author: Sean Owen <sowen@cloudera.com> Closes #15075 from srowen/SPARK-17445.
* [SPARKR][DOCS] fix broken url in docFelix Cheung2016-07-251-54/+53
| | | | | | | | | | | | | | | | | | | | ## 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.
* [SPARKR][DOCS] minor code sample update in R programming guideFelix Cheung2016-07-181-2/+2
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Fix code style from ad hoc review of RC4 doc ## How was this patch tested? manual shivaram Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #14250 from felixcheung/rdocs2rc4.
* [SPARK-16112][SPARKR] Programming guide for gapply/gapplyCollectNarine Kokhlikyan2016-07-161-4/+134
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Updates programming guide for spark.gapply/spark.gapplyCollect. Similar to other examples I used `faithful` dataset to demonstrate gapply's functionality. Please, let me know if you prefer another example. ## How was this patch tested? Existing test cases in R Author: Narine Kokhlikyan <narine@slice.com> Closes #14090 from NarineK/gapplyProgGuide.
* [SPARKR][DOCS][MINOR] R programming guide to include csv data source exampleFelix Cheung2016-07-131-9/+18
| | | | | | | | | | | | | | | | ## 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][DOC] SparkR ML user guides update for 2.0Yanbo Liang2016-07-111-18/+25
| | | | | | | | | | | | | ## 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-16088][SPARKR] update setJobGroup, cancelJobGroup, clearJobGroupFelix Cheung2016-06-231-0/+2
| | | | | | | | | | | | | | | ## 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 Jiang2016-06-221-0/+77
| | | | | | | | | | | | | | | ## 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-15863][SQL][DOC][SPARKR] sql programming guide updates to include ↵Felix Cheung2016-06-211-1/+1
| | | | | | | | | | | | | | | | | | sparkSession in R ## What changes were proposed in this pull request? Update doc as per discussion in PR #13592 ## How was this patch tested? manual shivaram liancheng Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #13799 from felixcheung/rsqlprogrammingguide.
* [SPARK-15159][SPARKR] SparkSession roxygen2 doc, programming guide, example ↵Felix Cheung2016-06-201-51/+48
| | | | | | | | | | | | | | | | | 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-15129][R][DOC] R API changes in MLGayathriMurali2016-06-171-58/+19
| | | | | | | | | | ## What changes were proposed in this pull request? Make user guide changes to SparkR documentation for all changes that happened in 2.0 to Machine Learning APIs Author: GayathriMurali <gayathri.m@intel.com> Closes #13285 from GayathriMurali/SPARK-15129.
* [SPARK-10903] followup - update API doc for SqlContextfelixcheung2016-05-261-0/+1
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Follow up on the earlier PR - in here we are fixing up roxygen2 doc examples. Also add to the programming guide migration section. ## How was this patch tested? SparkR tests Author: felixcheung <felixcheung_m@hotmail.com> Closes #13340 from felixcheung/sqlcontextdoc.
* [SPARK-12071][DOC] Document the behaviour of NA in RKrishna Kalyan2016-05-241-0/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Under Upgrading From SparkR 1.5.x to 1.6.x section added the information, SparkSQL converts `NA` in R to `null`. ## How was this patch tested? Document update, no tests. Author: Krishna Kalyan <krishnakalyan3@gmail.com> Closes #13268 from krishnakalyan3/spark-12071-1.
* [MINOR] [SPARKR] Update data-manipulation.R to use native csv readerYanbo Liang2016-05-091-2/+2
| | | | | | | | | | | | | ## What changes were proposed in this pull request? * Since Spark has supported native csv reader, it does not necessary to use the third party ```spark-csv``` in ```examples/src/main/r/data-manipulation.R```. Meanwhile, remove all ```spark-csv``` usage in SparkR. * Running R applications through ```sparkR``` is not supported as of Spark 2.0, so we change to use ```./bin/spark-submit``` to run the example. ## How was this patch tested? Offline test. Author: Yanbo Liang <ybliang8@gmail.com> Closes #13005 from yanboliang/r-df-examples.
* [SPARK-14883][DOCS] Fix wrong R examples and make them up-to-dateDongjoon Hyun2016-04-241-6/+5
| | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This issue aims to fix some errors in R examples and make them up-to-date in docs and example modules. - Remove the wrong usage of `map`. We need to use `lapply` in `sparkR` if needed. However, `lapply` is private so far. The corrected example will be added later. - Fix the wrong example in Section `Generic Load/Save Functions` of `docs/sql-programming-guide.md` for consistency - Fix datatypes in `sparkr.md`. - Update a data result in `sparkr.md`. - Replace deprecated functions to remove warnings: jsonFile -> read.json, parquetFile -> read.parquet - Use up-to-date R-like functions: loadDF -> read.df, saveDF -> write.df, saveAsParquetFile -> write.parquet - Replace `SparkR DataFrame` with `SparkDataFrame` in `dataframe.R` and `data-manipulation.R`. - Other minor syntax fixes and a typo. ## How was this patch tested? Manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #12649 from dongjoon-hyun/SPARK-14883.
* [SPARK-12148][SPARKR] fix doc after renaming DataFrame to SparkDataFramefelixcheung2016-04-231-2/+3
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Fixed inadvertent roxygen2 doc changes, added class name change to programming guide Follow up of #12621 ## How was this patch tested? manually checked Author: felixcheung <felixcheung_m@hotmail.com> Closes #12647 from felixcheung/rdataframe.
* [SPARK-12232][SPARKR] New R API for read.table to avoid name conflictfelixcheung2016-01-191-7/+4
| | | | | | | | shivaram sorry it took longer to fix some conflicts, this is the change to add an alias for `table` Author: felixcheung <felixcheung_m@hotmail.com> Closes #10406 from felixcheung/readtable.
* [SPARKR][DOC] minor doc update for version in migration guidefelixcheung2016-01-051-3/+3
| | | | | | | | | checked that the change is in Spark 1.6.0. shivaram Author: felixcheung <felixcheung_m@hotmail.com> Closes #10574 from felixcheung/rwritemodedoc.
* [SPARK-12318][SPARKR] Save mode in SparkR should be error by defaultJeff Zhang2015-12-161-1/+8
| | | | | | | | shivaram Please help review. Author: Jeff Zhang <zjffdu@apache.org> Closes #10290 from zjffdu/SPARK-12318.
* [SPARK-12116][SPARKR][DOCS] document how to workaround function name ↵felixcheung2015-12-031-1/+2
| | | | | | | | | | conflicts with dplyr shivaram Author: felixcheung <felixcheung_m@hotmail.com> Closes #10119 from felixcheung/rdocdplyrmasked.
* [SPARK-11339][SPARKR] Document the list of functions in R base package that ↵felixcheung2015-11-181-1/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | are masked by functions with same name in SparkR Added tests for function that are reported as masked, to make sure the base:: or stats:: function can be called. For those we can't call, added them to SparkR programming guide. It would seem to me `table, sample, subset, filter, cov` not working are not actually expected - I investigated/experimented with them but couldn't get them to work. It looks like as they are defined in base or stats they are missing the S3 generic, eg. ``` > methods("transform") [1] transform,ANY-method transform.data.frame [3] transform,DataFrame-method transform.default see '?methods' for accessing help and source code > methods("subset") [1] subset.data.frame subset,DataFrame-method subset.default [4] subset.matrix see '?methods' for accessing help and source code Warning message: In .S3methods(generic.function, class, parent.frame()) : function 'subset' appears not to be S3 generic; found functions that look like S3 methods ``` Any idea? More information on masking: http://www.ats.ucla.edu/stat/r/faq/referencing_objects.htm http://www.sfu.ca/~sweldon/howTo/guide4.pdf This is what the output doc looks like (minus css): ![image](https://cloud.githubusercontent.com/assets/8969467/11229714/2946e5de-8d4d-11e5-94b0-dda9696b6fdd.png) Author: felixcheung <felixcheung_m@hotmail.com> Closes #9785 from felixcheung/rmasked.
* [SPARK-11684][R][ML][DOC] Update SparkR glm API doc, user guide and example ↵Yanbo Liang2015-11-181-8/+42
| | | | | | | | | | | | | | | | | codes This PR includes: * Update SparkR:::glm, SparkR:::summary API docs. * Update SparkR machine learning user guide and example codes to show: * supporting feature interaction in R formula. * summary for gaussian GLM model. * coefficients for binomial GLM model. mengxr Author: Yanbo Liang <ybliang8@gmail.com> Closes #9727 from yanboliang/spark-11684.
* [SPARK-11407][SPARKR] Add doc for running from RStudiofelixcheung2015-11-031-3/+43
| | | | | | | | | | ![image](https://cloud.githubusercontent.com/assets/8969467/10871746/612ba44a-80a4-11e5-99a0-40b9931dee52.png) (This is without css, but you get the idea) shivaram Author: felixcheung <felixcheung_m@hotmail.com> Closes #9401 from felixcheung/rstudioprogrammingguide.
* [SPARK-11340][SPARKR] Support setting driver properties when starting Spark ↵felixcheung2015-10-301-8/+20
| | | | | | | | | | | | | from R programmatically or from RStudio Mapping spark.driver.memory from sparkEnvir to spark-submit commandline arguments. shivaram suggested that we possibly add other spark.driver.* properties - do we want to add all of those? I thought those could be set in SparkConf? sun-rui Author: felixcheung <felixcheung_m@hotmail.com> Closes #9290 from felixcheung/rdrivermem.
* [SPARK-9713] [ML] Document SparkR MLlib glm() integration in Spark 1.5Eric Liang2015-08-111-1/+36
| | | | | | | | | | This documents the use of R model formulae in the SparkR guide. Also fixes some bugs in the R api doc. mengxr Author: Eric Liang <ekl@databricks.com> Closes #8085 from ericl/docs.
* [SPARK-8900] [SPARKR] Fix sparkPackages in init documentationShivaram Venkataraman2015-07-081-1/+1
| | | | | | | | | | cc pwendell Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #7293 from shivaram/sparkr-packages-doc and squashes the following commits: c91471d [Shivaram Venkataraman] Fix sparkPackages in init documentation
* [SPARK-8894] [SPARKR] [DOC] Example code errors in SparkR documentation.Sun Rui2015-07-081-1/+1
| | | | | | | | Author: Sun Rui <rui.sun@intel.com> Closes #7287 from sun-rui/SPARK-8894 and squashes the following commits: da63898 [Sun Rui] [SPARK-8894][SPARKR][DOC] Example code errors in SparkR documentation.
* [SPARK-8506] Add pakages to R context created through init.Holden Karau2015-06-241-4/+13
| | | | | | | | | | | | | Author: Holden Karau <holden@pigscanfly.ca> Closes #6928 from holdenk/SPARK-8506-sparkr-does-not-provide-an-easy-way-to-depend-on-spark-packages-when-performing-init-from-inside-of-r and squashes the following commits: b60dd63 [Holden Karau] Add an example with the spark-csv package fa8bc92 [Holden Karau] typo: sparm -> spark 865a90c [Holden Karau] strip spaces for comparision c7a4471 [Holden Karau] Add some documentation c1a9233 [Holden Karau] refactor for testing c818556 [Holden Karau] Add pakages to R
* [SPARK-6806] [SPARKR] [DOCS] Add a new SparkR programming guideShivaram Venkataraman2015-05-291-0/+223
This PR adds a new SparkR programming guide at the top-level. This will be useful for R users as our APIs don't directly match the Scala/Python APIs and as we need to explain SparkR without using RDDs as examples etc. cc rxin davies pwendell cc cafreeman -- Would be great if you could also take a look at this ! Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6490 from shivaram/sparkr-guide and squashes the following commits: d5ff360 [Shivaram Venkataraman] Add a section on HiveContext, HQL queries 408dce5 [Shivaram Venkataraman] Fix link dbb86e3 [Shivaram Venkataraman] Fix minor typo 9aff5e0 [Shivaram Venkataraman] Address comments, use dplyr-like syntax in example d09703c [Shivaram Venkataraman] Fix default argument in read.df ea816a1 [Shivaram Venkataraman] Add a new SparkR programming guide Also update write.df, read.df to handle defaults better
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