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* [SPARK-6797] [SPARKR] Add support for YARN cluster mode.Sun Rui2015-07-138-38/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR enables SparkR to dynamically ship the SparkR binary package to the AM node in YARN cluster mode, thus it is no longer required that the SparkR package be installed on each worker node. This PR uses the JDK jar tool to package the SparkR package, because jar is thought to be available on both Linux/Windows platforms where JDK has been installed. This PR does not address the R worker involved in RDD API. Will address it in a separate JIRA issue. This PR does not address SBT build. SparkR installation and packaging by SBT will be addressed in a separate JIRA issue. R/install-dev.bat is not tested. shivaram , Could you help to test it? Author: Sun Rui <rui.sun@intel.com> Closes #6743 from sun-rui/SPARK-6797 and squashes the following commits: ca63c86 [Sun Rui] Adjust MimaExcludes after rebase. 7313374 [Sun Rui] Fix unit test errors. 72695fb [Sun Rui] Fix unit test failures. 193882f [Sun Rui] Fix Mima test error. fe25a33 [Sun Rui] Fix Mima test error. 35ecfa3 [Sun Rui] Fix comments. c38a005 [Sun Rui] Unzipped SparkR binary package is still required for standalone and Mesos modes. b05340c [Sun Rui] Fix scala style. 2ca5048 [Sun Rui] Fix comments. 1acefd1 [Sun Rui] Fix scala style. 0aa1e97 [Sun Rui] Fix scala style. 41d4f17 [Sun Rui] Add support for locating SparkR package for R workers required by RDD APIs. 49ff948 [Sun Rui] Invoke jar.exe with full path in install-dev.bat. 7b916c5 [Sun Rui] Use 'rem' consistently. 3bed438 [Sun Rui] Add a comment. 681afb0 [Sun Rui] Fix a bug that RRunner does not handle client deployment modes. cedfbe2 [Sun Rui] [SPARK-6797][SPARKR] Add support for YARN cluster mode.
* [SPARK-8940] [SPARKR] Don't overwrite given schema in createDataFrameLiang-Chi Hsieh2015-07-091-1/+3
| | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-8940 The given `schema` parameter will be overwritten in `createDataFrame` now. If it is not null, we shouldn't overwrite it. Author: Liang-Chi Hsieh <viirya@appier.com> Closes #7311 from viirya/df_not_overwrite_schema and squashes the following commits: 2385139 [Liang-Chi Hsieh] Don't overwrite given schema if it is not null.
* Small update in the readme fileDirceu Semighini Filho2015-07-061-1/+1
| | | | | | | | | | Just change the attribute from -PsparkR to -Psparkr Author: Dirceu Semighini Filho <dirceu.semighini@gmail.com> Closes #7242 from dirceusemighini/patch-1 and squashes the following commits: fad5991 [Dirceu Semighini Filho] Small update in the readme file
* [SPARK-8549] [SPARKR] Fix the line length of SparkRYu ISHIKAWA2015-07-057-31/+51
| | | | | | | | | | | [[SPARK-8549] Fix the line length of SparkR - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8549) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #7204 from yu-iskw/SPARK-8549 and squashes the following commits: 6fb131a [Yu ISHIKAWA] Fix the typo 1737598 [Yu ISHIKAWA] [SPARK-8549][SparkR] Fix the line length of SparkR
* [SPARK-3071] Increase default driver memoryIlya Ganelin2015-07-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | I've updated default values in comments, documentation, and in the command line builder to be 1g based on comments in the JIRA. I've also updated most usages to point at a single variable defined in the Utils.scala and JavaUtils.java files. This wasn't possible in all cases (R, shell scripts etc.) but usage in most code is now pointing at the same place. Please let me know if I've missed anything. Will the spark-shell use the value within the command line builder during instantiation? Author: Ilya Ganelin <ilya.ganelin@capitalone.com> Closes #7132 from ilganeli/SPARK-3071 and squashes the following commits: 4074164 [Ilya Ganelin] String fix 271610b [Ilya Ganelin] Merge branch 'SPARK-3071' of github.com:ilganeli/spark into SPARK-3071 273b6e9 [Ilya Ganelin] Test fix fd67721 [Ilya Ganelin] Update JavaUtils.java 26cc177 [Ilya Ganelin] test fix e5db35d [Ilya Ganelin] Fixed test failure 39732a1 [Ilya Ganelin] merge fix a6f7deb [Ilya Ganelin] Created default value for DRIVER MEM in Utils that's now used in almost all locations instead of setting manually in each 09ad698 [Ilya Ganelin] Update SubmitRestProtocolSuite.scala 19b6f25 [Ilya Ganelin] Missed one doc update 2698a3d [Ilya Ganelin] Updated default value for driver memory
* [SPARK-7714] [SPARKR] SparkR tests should use more specific expectations ↵Sun Rui2015-07-019-194/+194
| | | | | | | | | | | | | | | | | than expect_true 1. Update the pattern 'expect_true(a == b)' to 'expect_equal(a, b)'. 2. Update the pattern 'expect_true(inherits(a, b))' to 'expect_is(a, b)'. 3. Update the pattern 'expect_true(identical(a, b))' to 'expect_identical(a, b)'. Author: Sun Rui <rui.sun@intel.com> Closes #7152 from sun-rui/SPARK-7714 and squashes the following commits: 8ad2440 [Sun Rui] Fix test case errors. 8fe9f0c [Sun Rui] Update the pattern 'expect_true(identical(a, b))' to 'expect_identical(a, b)'. f1b8005 [Sun Rui] Update the pattern 'expect_true(inherits(a, b))' to 'expect_is(a, b)'. f631e94 [Sun Rui] Update the pattern 'expect_true(a == b)' to 'expect_equal(a, b)'.
* [SPARK-8434][SQL]Add a "pretty" parameter to the "show" method to display ↵zsxwing2015-06-291-2/+2
| | | | | | | | | | | | | | | | | | | | | | | long strings Sometimes the user may want to show the complete content of cells. Now `sql("set -v").show()` displays: ![screen shot 2015-06-18 at 4 34 51 pm](https://cloud.githubusercontent.com/assets/1000778/8227339/14d3c5ea-15d9-11e5-99b9-f00b7e93beef.png) The user needs to use something like `sql("set -v").collect().foreach(r => r.toSeq.mkString("\t"))` to show the complete content. This PR adds a `pretty` parameter to show. If `pretty` is false, `show` won't truncate strings or align cells right. ![screen shot 2015-06-18 at 4 21 44 pm](https://cloud.githubusercontent.com/assets/1000778/8227407/b6f8dcac-15d9-11e5-8219-8079280d76fc.png) Author: zsxwing <zsxwing@gmail.com> Closes #6877 from zsxwing/show and squashes the following commits: 22e28e9 [zsxwing] pretty -> truncate e582628 [zsxwing] Add pretty parameter to the show method in R a3cd55b [zsxwing] Fix calling showString in R 923cee4 [zsxwing] Add a "pretty" parameter to show to display long strings
* [SPARK-8607] SparkR -- jars not being added to application classpath correctlycafreeman2015-06-263-0/+69
| | | | | | | | | | | | | | | | | | | | | | | | | Add `getStaticClass` method in SparkR's `RBackendHandler` This is a fix for the problem referenced in [SPARK-5185](https://issues.apache.org/jira/browse/SPARK-5185). cc shivaram Author: cafreeman <cfreeman@alteryx.com> Closes #7001 from cafreeman/branch-1.4 and squashes the following commits: 8f81194 [cafreeman] Add missing license 31aedcf [cafreeman] Refactor test to call an external R script 2c22073 [cafreeman] Merge branch 'branch-1.4' of github.com:apache/spark into branch-1.4 0bea809 [cafreeman] Fixed relative path issue and added smaller JAR ee25e60 [cafreeman] Merge branch 'branch-1.4' of github.com:apache/spark into branch-1.4 9a5c362 [cafreeman] test for including JAR when launching sparkContext 9101223 [cafreeman] Merge branch 'branch-1.4' of github.com:apache/spark into branch-1.4 5a80844 [cafreeman] Fix style nits 7c6bd0c [cafreeman] [SPARK-8607] SparkR (cherry picked from commit 2579948bf5d89ac2d822ace605a6a4afce5258d6) Signed-off-by: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
* [SPARK-8662] SparkR Update SparkSQL Testcafreeman2015-06-261-3/+12
| | | | | | | | | | | | | | | | | Test `infer_type` using a more fine-grained approach rather than comparing environments. Since `all.equal`'s behavior has changed in R 3.2, the test became unpassable. JIRA here: https://issues.apache.org/jira/browse/SPARK-8662 Author: cafreeman <cfreeman@alteryx.com> Closes #7045 from cafreeman/R32_Test and squashes the following commits: b97cc52 [cafreeman] Add `checkStructField` utility 3381e5c [cafreeman] Update SparkSQL Test (cherry picked from commit 78b31a2a630c2178987322d0221aeea183ec565f) Signed-off-by: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
* [SPARK-8637] [SPARKR] [HOTFIX] Fix packages argument, sparkSubmitBinNameShivaram Venkataraman2015-06-252-2/+2
| | | | | | | | | | cc cafreeman Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #7022 from shivaram/sparkr-init-hotfix and squashes the following commits: 9178d15 [Shivaram Venkataraman] Fix packages argument, sparkSubmitBinName
* [SPARK-8506] Add pakages to R context created through init.Holden Karau2015-06-243-9/+56
| | | | | | | | | | | | | 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-8111] [SPARKR] SparkR shell should display Spark logo and version ↵Alok Singh2015-06-231-1/+15
| | | | | | | | | | | | | | banner on startup. spark version is taken from the environment variable SPARK_VERSION Author: Alok Singh <singhal@Aloks-MacBook-Pro.local> Author: Alok Singh <singhal@aloks-mbp.usca.ibm.com> Closes #6944 from aloknsingh/aloknsingh_spark_jiras and squashes the following commits: ed607bd [Alok Singh] [SPARK-8111][SparkR] As per suggestion, 1) using the version from sparkContext rather than the Sys.env. 2) change "Welcome to SparkR!" to "Welcome to" followed by Spark logo and version acd5b85 [Alok Singh] fix the jira SPARK-8111 to add the spark version and logo. Currently spark version is taken from the environment variable SPARK_VERSION
* [SPARK-8431] [SPARKR] Add in operator to DataFrame Column in SparkRYu ISHIKAWA2015-06-222-0/+26
| | | | | | | | | | | | | [[SPARK-8431] Add in operator to DataFrame Column in SparkR - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8431) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6941 from yu-iskw/SPARK-8431 and squashes the following commits: 1f64423 [Yu ISHIKAWA] Modify the comment f4309a7 [Yu ISHIKAWA] Make a `setMethod` for `%in%` be independent 6e37936 [Yu ISHIKAWA] Modify a variable name c196173 [Yu ISHIKAWA] [SPARK-8431][SparkR] Add in operator to DataFrame Column in SparkR
* [SPARK-8548] [SPARKR] Remove the trailing whitespaces from the SparkR filesYu ISHIKAWA2015-06-2222-188/+182
| | | | | | | | | | | | | [[SPARK-8548] Remove the trailing whitespaces from the SparkR files - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8548) - This is the result of `lint-r` https://gist.github.com/yu-iskw/0019b37a2c1167f33986 Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6945 from yu-iskw/SPARK-8548 and squashes the following commits: 0bd567a [Yu ISHIKAWA] [SPARK-8548][SparkR] Remove the trailing whitespaces from the SparkR files
* [SPARK-8537] [SPARKR] Add a validation rule about the curly braces in SparkR ↵Yu ISHIKAWA2015-06-221-1/+1
| | | | | | | | | | | | to `.lintr` [[SPARK-8537] Add a validation rule about the curly braces in SparkR to `.lintr` - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8537) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6940 from yu-iskw/SPARK-8537 and squashes the following commits: 7eec1a0 [Yu ISHIKAWA] [SPARK-8537][SparkR] Add a validation rule about the curly braces in SparkR to `.lintr`
* [SPARK-8495] [SPARKR] Add a `.lintr` file to validate the SparkR files and ↵Yu ISHIKAWA2015-06-201-0/+2
| | | | | | | | | | | | | | the `lint-r` script Thank Shivaram Venkataraman for your support. This is a prototype script to validate the R files. Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6922 from yu-iskw/SPARK-6813 and squashes the following commits: c1ffe6b [Yu ISHIKAWA] Modify to save result to a log file and add a rule to validate 5520806 [Yu ISHIKAWA] Exclude the .lintr file not to check Apache lincence 8f94680 [Yu ISHIKAWA] [SPARK-8495][SparkR] Add a `.lintr` file to validate the SparkR files and the `lint-r` script
* [SPARK-8452] [SPARKR] expose jobGroup API in SparkRHossein2015-06-193-0/+56
| | | | | | | | | | | | | | | | | | | | | | This pull request adds following methods to SparkR: ```R setJobGroup() cancelJobGroup() clearJobGroup() ``` For each method, the spark context is passed as the first argument. There does not seem to be a good way to test these in R. cc shivaram and davies Author: Hossein <hossein@databricks.com> Closes #6889 from falaki/SPARK-8452 and squashes the following commits: 9ce9f1e [Hossein] Added basic tests to verify methods can be called and won't throw errors c706af9 [Hossein] Added examples a2c19af [Hossein] taking spark context as first argument 343ca77 [Hossein] Added setJobGroup, cancelJobGroup and clearJobGroup to SparkR
* [SPARK-8350] [R] Log R unit test output to "unit-tests.log"andrewor142015-06-151-1/+1
| | | | | | | | | | | | | | | | | Right now it's logged to "R-unit-tests.log". Jenkins currently only archives files named "unit-tests.log", and this is what all other modules (e.g. SQL, network, REPL) use. 1. We should be consistent 2. I don't want to reconfigure Jenkins to accept a different file shivaram Author: andrewor14 <andrew@databricks.com> Author: Andrew Or <andrew@databricks.com> Closes #6807 from andrewor14/r-logs and squashes the following commits: 96005d2 [andrewor14] Nest unit-tests.log further until R 407c46c [andrewor14] Add target to log path d7b68ae [Andrew Or] Log R unit test output to "unit-tests.log"
* [SPARK-6820] [SPARKR] Convert NAs to null type in SparkR DataFrameshqzizania2015-06-082-0/+45
| | | | | | | | | Author: hqzizania <qian.huang@intel.com> Closes #6190 from hqzizania/R and squashes the following commits: 1641f9e [hqzizania] fixes and add test units bb3411a [hqzizania] Convert NAs to null type in SparkR DataFrames
* [SPARK-8085] [SPARKR] Support user-specified schema in read.dfShivaram Venkataraman2015-06-052-4/+23
| | | | | | | | | | | | cc davies sun-rui Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6620 from shivaram/sparkr-read-schema and squashes the following commits: 16a6726 [Shivaram Venkataraman] Fix loadDF to pass schema Also add a unit test a229877 [Shivaram Venkataraman] Use wrapper function to DataFrameReader ee70ba8 [Shivaram Venkataraman] Support user-specified schema in read.df
* [SPARK-8027] [SPARKR] Move man pages creation to install-dev.shShivaram Venkataraman2015-06-042-5/+9
| | | | | | | | | | | | | | | This also helps us get rid of the sparkr-docs maven profile as docs are now built by just using -Psparkr when the roxygen2 package is available Related to discussion in #6567 cc pwendell srowen -- Let me know if this looks better Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6593 from shivaram/sparkr-pom-cleanup and squashes the following commits: b282241 [Shivaram Venkataraman] Remove sparkr-docs from release script as well 8f100a5 [Shivaram Venkataraman] Move man pages creation to install-dev.sh This also helps us get rid of the sparkr-docs maven profile as docs are now built by just using -Psparkr when the roxygen2 package is available
* [SPARK-8084] [SPARKR] Make SparkR scripts fail on errorShivaram Venkataraman2015-06-032-0/+5
| | | | | | | | | | cc shaneknapp pwendell JoshRosen Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6623 from shivaram/SPARK-8084 and squashes the following commits: 0ec5b26 [Shivaram Venkataraman] Make SparkR scripts fail on error
* [SPARK-8063] [SPARKR] Spark master URL conflict between MASTER env variable ↵Sun Rui2015-06-031-1/+1
| | | | | | | | | | and --master command line option. Author: Sun Rui <rui.sun@intel.com> Closes #6605 from sun-rui/SPARK-8063 and squashes the following commits: 51ca48b [Sun Rui] [SPARK-8063][SPARKR] Spark master URL conflict between MASTER env variable and --master command line option.
* [SPARK-7227] [SPARKR] Support fillna / dropna in R DataFrame.Sun Rui2015-05-315-1/+263
| | | | | | | | | Author: Sun Rui <rui.sun@intel.com> Closes #6183 from sun-rui/SPARK-7227 and squashes the following commits: dd6f5b3 [Sun Rui] Rename readEnv() back to readMap(). Add alias na.omit() for dropna(). 41cf725 [Sun Rui] [SPARK-7227][SPARKR] Support fillna / dropna in R DataFrame.
* [SPARK-7954] [SPARKR] Create SparkContext in sparkRSQL initShivaram Venkataraman2015-05-291-5/+19
| | | | | | | | | | cc davies Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6507 from shivaram/sparkr-init and squashes the following commits: 6fdd169 [Shivaram Venkataraman] Create SparkContext in sparkRSQL init
* [SPARK-6806] [SPARKR] [DOCS] Add a new SparkR programming guideShivaram Venkataraman2015-05-293-8/+11
| | | | | | | | | | | | | | | | | | | 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
* [SPARK-6811] Copy SparkR lib in make-distribution.shShivaram Venkataraman2015-05-235-2/+41
| | | | | | | | | | | | | | This change also remove native libraries from SparkR to make sure our distribution works across platforms Tested by building on Mac, running on Amazon Linux (CentOS), Windows VM and vice-versa (built on Linux run on Mac) I will also test this with YARN soon and update this PR. Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6373 from shivaram/sparkr-binary and squashes the following commits: ae41b5c [Shivaram Venkataraman] Remove native libraries from SparkR Also include the built SparkR package in make-distribution.sh
* [SPARK-6806] [SPARKR] [DOCS] Fill in SparkR examples in programming guideDavies Liu2015-05-238-262/+261
| | | | | | | | | | | | | | | | | | | | | | | | | | | | sqlCtx -> sqlContext You can check the docs by: ``` $ cd docs $ SKIP_SCALADOC=1 jekyll serve ``` cc shivaram Author: Davies Liu <davies@databricks.com> Closes #5442 from davies/r_docs and squashes the following commits: 7a12ec6 [Davies Liu] remove rdd in R docs 8496b26 [Davies Liu] remove the docs related to RDD e23b9d6 [Davies Liu] delete R docs for RDD API 222e4ff [Davies Liu] Merge branch 'master' into r_docs 89684ce [Davies Liu] Merge branch 'r_docs' of github.com:davies/spark into r_docs f0a10e1 [Davies Liu] address comments from @shivaram f61de71 [Davies Liu] Update pairRDD.R 3ef7cf3 [Davies Liu] use + instead of function(a,b) a+b 2f10a77 [Davies Liu] address comments from @cafreeman 9c2a062 [Davies Liu] mention R api together with Python API 23f751a [Davies Liu] Fill in SparkR examples in programming guide
* [SPARK-7687] [SQL] DataFrame.describe() should cast all aggregates to StringJosh Rosen2015-05-181-5/+5
| | | | | | | | | | | | | In `DataFrame.describe()`, the `count` aggregate produces an integer, the `avg` and `stdev` aggregates produce doubles, and `min` and `max` aggregates can produce varying types depending on what type of column they're applied to. As a result, we should cast all aggregate results to String so that `describe()`'s output types match its declared output schema. Author: Josh Rosen <joshrosen@databricks.com> Closes #6218 from JoshRosen/SPARK-7687 and squashes the following commits: 146b615 [Josh Rosen] Fix R test. 2974bd5 [Josh Rosen] Cast to string type instead f206580 [Josh Rosen] Cast to double to fix SPARK-7687 307ecbf [Josh Rosen] Add failing regression test for SPARK-7687
* [SPARK-7226] [SPARKR] Support math functions in R DataFrameqhuang2015-05-154-3/+100
| | | | | | | | | | Author: qhuang <qian.huang@intel.com> Closes #6170 from hqzizania/master and squashes the following commits: f20c39f [qhuang] add tests units and fixes 2a7d121 [qhuang] use a function name more familiar to R users 07aa72e [qhuang] Support math functions in R DataFrame
* [SPARK-7482] [SPARKR] Rename some DataFrame API methods in SparkR to match ↵Sun Rui2015-05-126-49/+71
| | | | | | | | | | | | their counterparts in Scala. Author: Sun Rui <rui.sun@intel.com> Closes #6007 from sun-rui/SPARK-7482 and squashes the following commits: 5c5cf5e [Sun Rui] Implement alias loadDF() as a new function. 3a30c10 [Sun Rui] Rename load()/save() to read.df()/write.df(). Also add loadDF()/saveDF() as aliases. 9f569d6 [Sun Rui] [SPARK-7482][SparkR] Rename some DataFrame API methods in SparkR to match their counterparts in Scala.
* [SPARK-7435] [SPARKR] Make DataFrame.show() consistent with that of Scala ↵Joshi2015-05-112-4/+6
| | | | | | | | | | | | | and pySpark Author: Joshi <rekhajoshm@gmail.com> Author: Rekha Joshi <rekhajoshm@gmail.com> Closes #5989 from rekhajoshm/fix/SPARK-7435 and squashes the following commits: cfc9e02 [Joshi] Spark-7435[R]: updated patch for review comments 62becc1 [Joshi] SPARK-7435: Update to DataFrame e3677c9 [Rekha Joshi] Merge pull request #1 from apache/master
* [SPARK-7462] By default retain group by columns in aggregateReynold Xin2015-05-111-3/+1
| | | | | | | | | | | | | | | | | Updated Java, Scala, Python, and R. Author: Reynold Xin <rxin@databricks.com> Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #5996 from rxin/groupby-retain and squashes the following commits: aac7119 [Reynold Xin] Merge branch 'groupby-retain' of github.com:rxin/spark into groupby-retain f6858f6 [Reynold Xin] Merge branch 'master' into groupby-retain 5f923c0 [Reynold Xin] Merge pull request #15 from shivaram/sparkr-groupby-retrain c1de670 [Shivaram Venkataraman] Revert workaround in SparkR to retain grouped cols Based on reverting code added in commit https://github.com/amplab-extras/spark/commit/9a6be746efc9fafad88122fa2267862ef87aa0e1 b8b87e1 [Reynold Xin] Fixed DataFrameJoinSuite. d910141 [Reynold Xin] Updated rest of the files 1e6e666 [Reynold Xin] [SPARK-7462] By default retain group by columns in aggregate
* [SPARK-7512] [SPARKR] Fix RDD's show method to use getJRDDShivaram Venkataraman2015-05-101-2/+2
| | | | | | | | | | | | | | | Since the RDD object might be a Pipelined RDD we should use `getJRDD` to get the right handle to the Java object. Fixes the bug reported at http://stackoverflow.com/questions/30057702/sparkr-filterrdd-and-flatmap-not-working cc concretevitamin Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6035 from shivaram/sparkr-show-bug and squashes the following commits: d70145c [Shivaram Venkataraman] Fix RDD's show method to use getJRDD Fixes the bug reported at http://stackoverflow.com/questions/30057702/sparkr-filterrdd-and-flatmap-not-working
* [SPARK-7231] [SPARKR] Changes to make SparkR DataFrame dplyr friendly.Shivaram Venkataraman2015-05-086-29/+228
| | | | | | | | | | | | | | | | | | | | | | Changes include 1. Rename sortDF to arrange 2. Add new aliases `group_by` and `sample_frac`, `summarize` 3. Add more user friendly column addition (mutate), rename 4. Support mean as an alias for avg in Scala and also support n_distinct, n as in dplyr Using these changes we can pretty much run the examples as described in http://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html with the same syntax The only thing missing in SparkR is auto resolving column names when used in an expression i.e. making something like `select(flights, delay)` works in dply but we right now need `select(flights, flights$delay)` or `select(flights, "delay")`. But this is a complicated change and I'll file a new issue for it cc sun-rui rxin Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #6005 from shivaram/sparkr-df-api and squashes the following commits: 5e0716a [Shivaram Venkataraman] Fix some roxygen bugs 1254953 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/apache/spark into sparkr-df-api 0521149 [Shivaram Venkataraman] Changes to make SparkR DataFrame dplyr friendly. Changes include 1. Rename sortDF to arrange 2. Add new aliases `group_by` and `sample_frac`, `summarize` 3. Add more user friendly column addition (mutate), rename 4. Support mean as an alias for avg in Scala and also support n_distinct, n as in dplyr
* [SPARK-6824] Fill the docs for DataFrame API in SparkRhqzizania2015-05-089-1609/+1610
| | | | | | | | | | | | | | | | | This patch also removes the RDD docs from being built as a part of roxygen just by the method to delete " ' '" of " \#' ". Author: hqzizania <qian.huang@intel.com> Author: qhuang <qian.huang@intel.com> Closes #5969 from hqzizania/R1 and squashes the following commits: 6d27696 [qhuang] fixes in NAMESPACE eb4b095 [qhuang] remove more docs 6394579 [qhuang] remove RDD docs in generics.R 6813860 [hqzizania] Fill the docs for DataFrame API in SparkR 857220f [hqzizania] remove the pairRDD docs from being built as a part of roxygen c045d64 [hqzizania] remove the RDD docs from being built as a part of roxygen
* [SPARK-6812] [SPARKR] filter() on DataFrame does not work as expected.Sun Rui2015-05-061-4/+6
| | | | | | | | | | | | | | | According to the R manual: https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html, " if a function .First is found on the search path, it is executed as .First(). Finally, function .First.sys() in the base package is run. This calls require to attach the default packages specified by options("defaultPackages")." In .First() in profile/shell.R, we load SparkR package. This means SparkR package is loaded before default packages. If there are same names in default packages, they will overwrite those in SparkR. This is why filter() in SparkR is masked by filter() in stats, which is usually in the default package list. We need to make sure SparkR is loaded after default packages. The solution is to append SparkR to default packages, instead of loading SparkR in .First(). BTW, I'd like to discuss our policy on how to solve name conflict. Previously, we rename API names from Scala API if there is name conflict with base or other commonly-used packages. However, from long term perspective, this is not good for API stability, because we can't predict name conflicts, for example, if in the future a name added in base package conflicts with an API in SparkR? So the better policy is to keep API name same as Scala's without worrying about name conflicts. When users use SparkR, they should load SparkR as last package, so that all API names are effective. Use can explicitly use :: to refer to hidden names from other packages. If we agree on this, I can submit a JIRA issue to change back some rename API methods, for example, DataFrame.sortDF(). Author: Sun Rui <rui.sun@intel.com> Closes #5938 from sun-rui/SPARK-6812 and squashes the following commits: b569145 [Sun Rui] [SPARK-6812][SparkR] filter() on DataFrame does not work as expected.
* [SPARK-6799] [SPARKR] Remove SparkR RDD examples, add dataframe examplesShivaram Venkataraman2015-05-062-5/+1
| | | | | | | | | | | | This PR also makes some of the DataFrame to RDD methods private as the RDD class is private in 1.4 cc rxin pwendell Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #5949 from shivaram/sparkr-examples and squashes the following commits: 6c42fdc [Shivaram Venkataraman] Remove SparkR RDD examples, add dataframe examples
* [SPARK-6841] [SPARKR] add support for mean, median, stdev etc.qhuang2015-05-054-0/+53
| | | | | | | | | | | | | | Moving here from https://github.com/amplab-extras/SparkR-pkg/pull/241 sum() has been implemented. (https://github.com/amplab-extras/SparkR-pkg/pull/242) Now Phase 1: mean, sd, var have been implemented, but some things still need to be improved with the suggestions in https://issues.apache.org/jira/browse/SPARK-6841 Author: qhuang <qian.huang@intel.com> Closes #5446 from hqzizania/R and squashes the following commits: f283572 [qhuang] add test unit for describe() 2e74d5a [qhuang] add describe() DataFrame API
* [SPARK-7230] [SPARKR] Make RDD private in SparkR.Shivaram Venkataraman2015-05-056-103/+26
| | | | | | | | | | This change makes the RDD API private in SparkR and all internal uses of the SparkR API use SparkR::: to access private functions. Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #5895 from shivaram/rrdd-private and squashes the following commits: bdb2f07 [Shivaram Venkataraman] Make RDD private in SparkR. This change also makes all internal uses of the SparkR API use SparkR::: to access private functions
* [SPARK-7319][SQL] Improve the output from DataFrame.show()云峤2015-05-042-2/+2
| | | | | | | | | | | | | | | | | | | | Author: 云峤 <chensong.cs@alibaba-inc.com> Closes #5865 from kaka1992/df.show and squashes the following commits: c79204b [云峤] Update a1338f6 [云峤] Update python dataFrame show test and add empty df unit test. 734369c [云峤] Update python dataFrame show test and add empty df unit test. 84aec3e [云峤] Update python dataFrame show test and add empty df unit test. 159b3d5 [云峤] update 03ef434 [云峤] update 7394fd5 [云峤] update test show ced487a [云峤] update pep8 b6e690b [云峤] Merge remote-tracking branch 'upstream/master' into df.show 30ac311 [云峤] [SPARK-7294] ADD BETWEEN 7d62368 [云峤] [SPARK-7294] ADD BETWEEN baf839b [云峤] [SPARK-7294] ADD BETWEEN d11d5b9 [云峤] [SPARK-7294] ADD BETWEEN
* [SPARK-6991] [SPARKR] Adds support for zipPartitions.hlin092015-04-274-0/+85
| | | | | | | | | | | Author: hlin09 <hlin09pu@gmail.com> Closes #5568 from hlin09/zipPartitions and squashes the following commits: 12c08a5 [hlin09] Fix comments d2d32db [hlin09] Merge branch 'master' into zipPartitions ec56d2f [hlin09] Fix test. 27655d3 [hlin09] Adds support for zipPartitions.
* [SPARK-6856] [R] Make RDD information more useful in SparkRJeff Harrison2015-04-272-0/+10
| | | | | | | | | | | | | Author: Jeff Harrison <jeffrharrison@gmail.com> Closes #5667 from His-name-is-Joof/joofspark and squashes the following commits: f8814a6 [Jeff Harrison] newline added after RDD show() output 4d9d972 [Jeff Harrison] Merge branch 'master' into joofspark 9d2295e [Jeff Harrison] parallelize with 1:10 878b830 [Jeff Harrison] Merge branch 'master' into joofspark c8c0b80 [Jeff Harrison] add test for RDD function show() 123be65 [Jeff Harrison] SPARK-6856
* [SPARK-6852] [SPARKR] Accept numeric as numPartitions in SparkR.Sun Rui2015-04-243-19/+19
| | | | | | | | | Author: Sun Rui <rui.sun@intel.com> Closes #5613 from sun-rui/SPARK-6852 and squashes the following commits: abaf02e [Sun Rui] Change the type of default numPartitions from integer to numeric in generics.R. 29d67c1 [Sun Rui] [SPARK-6852][SPARKR] Accept numeric as numPartitions in SparkR.
* [SPARK-7033] [SPARKR] Clean usage of split. Use partition instead where ↵Sun Rui2015-04-245-39/+39
| | | | | | | | | | | applicable. Author: Sun Rui <rui.sun@intel.com> Closes #5628 from sun-rui/SPARK-7033 and squashes the following commits: 046bc9e [Sun Rui] Clean split usage in tests. d531c86 [Sun Rui] [SPARK-7033][SPARKR] Clean usage of split. Use partition instead where applicable.
* [SPARK-6818] [SPARKR] Support column deletion in SparkR DataFrame API.Sun Rui2015-04-232-1/+12
| | | | | | | | Author: Sun Rui <rui.sun@intel.com> Closes #5655 from sun-rui/SPARK-6818 and squashes the following commits: 7c66570 [Sun Rui] [SPARK-6818][SPARKR] Support column deletion in SparkR DataFrame API.
* [SPARK-6807] [SparkR] Merge recent SparkR-pkg changescafreeman2015-04-1717-279/+866
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR pulls in recent changes in SparkR-pkg, including cartesian, intersection, sampleByKey, subtract, subtractByKey, except, and some API for StructType and StructField. Author: cafreeman <cfreeman@alteryx.com> Author: Davies Liu <davies@databricks.com> Author: Zongheng Yang <zongheng.y@gmail.com> Author: Shivaram Venkataraman <shivaram.venkataraman@gmail.com> Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Author: Sun Rui <rui.sun@intel.com> Closes #5436 from davies/R3 and squashes the following commits: c2b09be [Davies Liu] SQLTypes -> schema a5a02f2 [Davies Liu] Merge branch 'master' of github.com:apache/spark into R3 168b7fe [Davies Liu] sort generics b1fe460 [Davies Liu] fix conflict in README.md e74c04e [Davies Liu] fix schema.R 4f5ac09 [Davies Liu] Merge branch 'master' of github.com:apache/spark into R5 41f8184 [Davies Liu] rm man ae78312 [Davies Liu] Merge pull request #237 from sun-rui/SPARKR-154_3 1bdcb63 [Zongheng Yang] Updates to README.md. 5a553e7 [cafreeman] Use object attribute instead of argument 71372d9 [cafreeman] Update docs and examples 8526d2e71 [cafreeman] Remove `tojson` functions 6ef5f2d [cafreeman] Fix spacing 7741d66 [cafreeman] Rename the SQL DataType function 141efd8 [Shivaram Venkataraman] Merge pull request #245 from hqzizania/upstream 9387402 [Davies Liu] fix style 40199eb [Shivaram Venkataraman] Move except into sorted position 07d0dbc [Sun Rui] [SPARKR-244] Fix test failure after integration of subtract() and subtractByKey() for RDD. 7e8caa3 [Shivaram Venkataraman] Merge pull request #246 from hlin09/fixCombineByKey ed66c81 [cafreeman] Update `subtract` to work with `generics.R` f3ba785 [cafreeman] Fixed duplicate export 275deb4 [cafreeman] Update `NAMESPACE` and tests 1a3b63d [cafreeman] new version of `CreateDF` 836c4bf [cafreeman] Update `createDataFrame` and `toDF` be5d5c1 [cafreeman] refactor schema functions 40338a4 [Zongheng Yang] Merge pull request #244 from sun-rui/SPARKR-154_5 20b97a6 [Zongheng Yang] Merge pull request #234 from hqzizania/assist ba54e34 [Shivaram Venkataraman] Merge pull request #238 from sun-rui/SPARKR-154_4 c9497a3 [Shivaram Venkataraman] Merge pull request #208 from lythesia/master b317aa7 [Zongheng Yang] Merge pull request #243 from hqzizania/master 136a07e [Zongheng Yang] Merge pull request #242 from hqzizania/stats cd66603 [cafreeman] new line at EOF 8b76e81 [Shivaram Venkataraman] Merge pull request #233 from redbaron/fail-early-on-missing-dep 7dd81b7 [cafreeman] Documentation 0e2a94f [cafreeman] Define functions for schema and fields
* [SPARK-6855] [SPARKR] Set R includes to get the right collate order.Shivaram Venkataraman2015-04-166-5/+13
| | | | | | | | | | This prevents tools like devtools::document creating invalid collate orders Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #5462 from shivaram/collate-order and squashes the following commits: f3db562 [Shivaram Venkataraman] Set R includes to get the right collate order. This prevents tools like devtools::document creating invalid collate orders
* [Minor][SparkR] Minor refactor and removes redundancy related to cleanClosure.hlin092015-04-132-16/+4
| | | | | | | | | | | 1. Only use `cleanClosure` in creation of RRDDs. Normally, user and developer do not need to call `cleanClosure` in their function definition. 2. Removes redundant code (e.g. unnecessary wrapper functions) related to `cleanClosure`. Author: hlin09 <hlin09pu@gmail.com> Closes #5495 from hlin09/cleanClosureFix and squashes the following commits: 74ec303 [hlin09] Minor refactor and removes redundancy.
* [SPARK-6881][SparkR] Changes the checkpoint directory name.hlin092015-04-133-4/+5
| | | | | | | | | Author: hlin09 <hlin09pu@gmail.com> Closes #5493 from hlin09/fixCheckpointDir and squashes the following commits: e67fc40 [hlin09] Change to temp dir. 1f7ed9e [hlin09] Change the checkpoint dir name.
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