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* [SPARK-9248] [SPARKR] Closing curly-braces should always be on their own lineYuu ISHIKAWA2015-07-304-14/+19
| | | | | | | | | | | | | | ### JIRA [[SPARK-9248] Closing curly-braces should always be on their own line - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-9248) ## The result of `dev/lint-r` [The result of `dev/lint-r` for SPARK-9248 at the revistion:6175d6cfe795fbd88e3ee713fac375038a3993a8](https://gist.github.com/yu-iskw/96cadcea4ce664c41f81) Author: Yuu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #7795 from yu-iskw/SPARK-9248 and squashes the following commits: c8eccd3 [Yuu ISHIKAWA] [SPARK-9248][SparkR] Closing curly-braces should always be on their own line
* [SPARK-9391] [ML] Support minus, dot, and intercept operators in SparkR RFormulaEric Liang2015-07-282-1/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Adds '.', '-', and intercept parsing to RFormula. Also splits RFormulaParser into a separate file. Umbrella design doc here: https://docs.google.com/document/d/10NZNSEurN2EdWM31uFYsgayIPfCFHiuIu3pCWrUmP_c/edit?usp=sharing mengxr Author: Eric Liang <ekl@databricks.com> Closes #7707 from ericl/string-features-2 and squashes the following commits: 8588625 [Eric Liang] exclude complex types for . 8106ffe [Eric Liang] comments a9350bb [Eric Liang] s/var/val 9c50d4d [Eric Liang] Merge branch 'string-features' into string-features-2 581afb2 [Eric Liang] Merge branch 'master' into string-features 08ae539 [Eric Liang] Merge branch 'string-features' into string-features-2 f99131a [Eric Liang] comments cecec43 [Eric Liang] Merge branch 'string-features' into string-features-2 0bf3c26 [Eric Liang] update docs 4592df2 [Eric Liang] intercept supports 7412a2e [Eric Liang] Fri Jul 24 14:56:51 PDT 2015 3cf848e [Eric Liang] fix the parser 0556c2b [Eric Liang] Merge branch 'string-features' into string-features-2 c302a2c [Eric Liang] fix tests 9d1ac82 [Eric Liang] Merge remote-tracking branch 'upstream/master' into string-features e713da3 [Eric Liang] comments cd231a9 [Eric Liang] Wed Jul 22 17:18:44 PDT 2015 4d79193 [Eric Liang] revert to seq + distinct 169a085 [Eric Liang] tweak functional test a230a47 [Eric Liang] Merge branch 'master' into string-features 72bd6f3 [Eric Liang] fix merge d841cec [Eric Liang] Merge branch 'master' into string-features 5b2c4a2 [Eric Liang] Mon Jul 20 18:45:33 PDT 2015 b01c7c5 [Eric Liang] add test 8a637db [Eric Liang] encoder wip a1d03f4 [Eric Liang] refactor into estimator
* Use vector-friendly comparison for packages argument.trestletech2015-07-282-1/+5
| | | | | | | | | | | | | | | | | | Otherwise, `sparkR.init()` with multiple `sparkPackages` results in this warning: ``` Warning message: In if (packages != "") { : the condition has length > 1 and only the first element will be used ``` Author: trestletech <jeff.allen@trestletechnology.net> Closes #7701 from trestletech/compare-packages and squashes the following commits: 72c8b36 [trestletech] Correct function name. c52db0e [trestletech] Added test for multiple packages. 3aab1a7 [trestletech] Use vector-friendly comparison for packages argument.
* [SPARK-9230] [ML] Support StringType features in RFormulaEric Liang2015-07-271-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | This adds StringType feature support via OneHotEncoder. As part of this task it was necessary to change RFormula to an Estimator, so that factor levels could be determined from the training dataset. Not sure if I am using uids correctly here, would be good to get reviewer help on that. cc mengxr Umbrella design doc: https://docs.google.com/document/d/10NZNSEurN2EdWM31uFYsgayIPfCFHiuIu3pCWrUmP_c/edit# Author: Eric Liang <ekl@databricks.com> Closes #7574 from ericl/string-features and squashes the following commits: f99131a [Eric Liang] comments 0bf3c26 [Eric Liang] update docs c302a2c [Eric Liang] fix tests 9d1ac82 [Eric Liang] Merge remote-tracking branch 'upstream/master' into string-features e713da3 [Eric Liang] comments 4d79193 [Eric Liang] revert to seq + distinct 169a085 [Eric Liang] tweak functional test a230a47 [Eric Liang] Merge branch 'master' into string-features 72bd6f3 [Eric Liang] fix merge d841cec [Eric Liang] Merge branch 'master' into string-features 5b2c4a2 [Eric Liang] Mon Jul 20 18:45:33 PDT 2015 b01c7c5 [Eric Liang] add test 8a637db [Eric Liang] encoder wip a1d03f4 [Eric Liang] refactor into estimator
* [SPARK-9249] [SPARKR] local variable assigned but may not be usedYu ISHIKAWA2015-07-242-5/+2
| | | | | | | | | | | | [[SPARK-9249] local variable assigned but may not be used - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-9249) https://gist.github.com/yu-iskw/0e5b0253c11769457ea5 Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #7640 from yu-iskw/SPARK-9249 and squashes the following commits: 7a51cab [Yu ISHIKAWA] [SPARK-9249][SparkR] local variable assigned but may not be used
* [SPARK-9243] [Documentation] null -> zero in crosstab docXiangrui Meng2015-07-231-1/+1
| | | | | | | | | | We forgot to update doc. brkyvz Author: Xiangrui Meng <meng@databricks.com> Closes #7608 from mengxr/SPARK-9243 and squashes the following commits: 0ea3236 [Xiangrui Meng] null -> zero in crosstab doc
* [SPARK-8364] [SPARKR] Add crosstab to SparkR DataFramesXiangrui Meng2015-07-224-0/+46
| | | | | | | | | | | | | | | | Add `crosstab` to SparkR DataFrames, which takes two column names and returns a local R data.frame. This is similar to `table` in R. However, `table` in SparkR is used for loading SQL tables as DataFrames. The return type is data.frame instead table for `crosstab` to be compatible with Scala/Python. I couldn't run R tests successfully on my local. Many unit tests failed. So let's try Jenkins. Author: Xiangrui Meng <meng@databricks.com> Closes #7318 from mengxr/SPARK-8364 and squashes the following commits: d75e894 [Xiangrui Meng] fix tests 53f6ddd [Xiangrui Meng] fix tests f1348d6 [Xiangrui Meng] update test 47cb088 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-8364 5621262 [Xiangrui Meng] first version without test
* [SPARK-9201] [ML] Initial integration of MLlib + SparkR using RFormulaEric Liang2015-07-205-0/+124
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This exposes the SparkR:::glm() and SparkR:::predict() APIs. It was necessary to change RFormula to silently drop the label column if it was missing from the input dataset, which is kind of a hack but necessary to integrate with the Pipeline API. The umbrella design doc for MLlib + SparkR integration can be viewed here: https://docs.google.com/document/d/10NZNSEurN2EdWM31uFYsgayIPfCFHiuIu3pCWrUmP_c/edit mengxr Author: Eric Liang <ekl@databricks.com> Closes #7483 from ericl/spark-8774 and squashes the following commits: 3dfac0c [Eric Liang] update 17ef516 [Eric Liang] more comments 1753a0f [Eric Liang] make glm generic b0f50f8 [Eric Liang] equivalence test 550d56d [Eric Liang] export methods c015697 [Eric Liang] second pass 117949a [Eric Liang] comments 5afbc67 [Eric Liang] test label columns 6b7f15f [Eric Liang] Fri Jul 17 14:20:22 PDT 2015 3a63ae5 [Eric Liang] Fri Jul 17 13:41:52 PDT 2015 ce61367 [Eric Liang] Fri Jul 17 13:41:17 PDT 2015 0299c59 [Eric Liang] Fri Jul 17 13:40:32 PDT 2015 e37603f [Eric Liang] Fri Jul 17 12:15:03 PDT 2015 d417d0c [Eric Liang] Merge remote-tracking branch 'upstream/master' into spark-8774 29a2ce7 [Eric Liang] Merge branch 'spark-8774-1' into spark-8774 d1959d2 [Eric Liang] clarify comment 2db68aa [Eric Liang] second round of comments dc3c943 [Eric Liang] address comments 5765ec6 [Eric Liang] fix style checks 1f361b0 [Eric Liang] doc d33211b [Eric Liang] r support fb0826b [Eric Liang] [SPARK-8774] Add R model formula with basic support as a transformer
* [SPARK-9052] [SPARKR] Fix comments after curly bracesYu ISHIKAWA2015-07-212-16/+30
| | | | | | | | | | | | | | | | | | [[SPARK-9052] Fix comments after curly braces - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-9052) This is the full result of lintr at the rivision:011551620faa87107a787530f074af3d9be7e695. [[SPARK-9052] the result of lint-r at the revision:011551620faa87107a787530f074af3d9be7e695](https://gist.github.com/yu-iskw/e7246041b173a3f29482) This is the difference of the result between before and after. https://gist.github.com/yu-iskw/e7246041b173a3f29482/revisions Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #7440 from yu-iskw/SPARK-9052 and squashes the following commits: 015d738 [Yu ISHIKAWA] Fix the indentations and move the placement of commna 5cc30fe [Yu ISHIKAWA] Fix the indentation in a condition 4ead0e5 [Yu ISHIKAWA] [SPARK-9052][SparkR] Fix comments after curly braces
* [SPARK-9093] [SPARKR] Fix single-quotes strings in SparkRYu ISHIKAWA2015-07-175-12/+12
| | | | | | | | | | | | | [[SPARK-9093] Fix single-quotes strings in SparkR - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-9093) This is the result of lintr at the rivision:011551620faa87107a787530f074af3d9be7e695 [[SPARK-9093] The result of lintr at 011551620faa87107a787530f074af3d9be7e695](https://gist.github.com/yu-iskw/8c47acf3202796da4d01) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #7439 from yu-iskw/SPARK-9093 and squashes the following commits: 61c391e [Yu ISHIKAWA] [SPARK-9093][SparkR] Fix single-quotes strings in SparkR
* [SPARK-8807] [SPARKR] Add between operator in SparkRLiang-Chi Hsieh2015-07-154-0/+34
| | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-8807 Add between operator in SparkR. Author: Liang-Chi Hsieh <viirya@appier.com> Closes #7356 from viirya/add_r_between and squashes the following commits: 7f51b44 [Liang-Chi Hsieh] Add test for non-numeric column. c6a25c5 [Liang-Chi Hsieh] Add between function.
* [SPARK-8840] [SPARKR] Add float coercion on SparkRLiang-Chi Hsieh2015-07-153-0/+28
| | | | | | | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-8840 Currently the type coercion rules don't include float type. This PR simply adds it. Author: Liang-Chi Hsieh <viirya@appier.com> Closes #7280 from viirya/add_r_float_coercion and squashes the following commits: c86dc0e [Liang-Chi Hsieh] For comments. dbf0c1b [Liang-Chi Hsieh] Implicitly convert Double to Float based on provided schema. 733015a [Liang-Chi Hsieh] Add test case for DataFrame with float type. 30c2a40 [Liang-Chi Hsieh] Update test case. 52b5294 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into add_r_float_coercion 6f9159d [Liang-Chi Hsieh] Add another test case. 8db3244 [Liang-Chi Hsieh] schema also needs to support float. add test case. 0dcc992 [Liang-Chi Hsieh] Add float coercion on SparkR.
* [SPARK-8808] [SPARKR] Fix assignments in SparkR.Sun Rui2015-07-149-13/+13
| | | | | | | | | Author: Sun Rui <rui.sun@intel.com> Closes #7395 from sun-rui/SPARK-8808 and squashes the following commits: ce603bc [Sun Rui] Use '<-' instead of '='. 88590b1 [Sun Rui] Use '<-' instead of '='.
* [SPARK-6797] [SPARKR] Add support for YARN cluster mode.Sun Rui2015-07-136-36/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* [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-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-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 Liu2015-05-237-260/+259
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
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