[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
GitHub user echarles opened a pull request:

    https://github.com/apache/incubator-zeppelin/pull/702

    R and SparkR Support [WIP]

    ### What is this PR for?
   
    Implement R and SpakR Intepreter as part of the Spark Interpreter Group. It also implements R and Scala binding (in both directions).
   
    ### What type of PR is it?
   
    [Feature]
   
    ### Todos
   
    * [ ] - Documentation
    * [ ] - Unit test (if relevant, as we depend on R being available on the host)
    * [ ] - Assess licensing (a priori ok as we don't delive anything out of ASL2, but we should corectly phrase the NOTICE as we depend on non-ASL2 comptabile licenses (R) to run the interpreter).
   
    ### Is there a relevant Jira issue?
   
    https://issues.apache.org/jira/browse/ZEPPELIN-156 SparkR support
   
    ### How should this be tested?
   
    You need R available on the host running the notebook.
   
        For Centos: yum install R R-devel
        For Ubuntu: apt-get install r-base r-cran-rserve
   
    Install additional R packages:
   
    ```
    curl https://cran.r-project.org/src/contrib/Archive/rscala/rscala_1.0.6.tar.gz -o /tmp/rscala_1.0.6.tar.gz
    R CMD INSTALL /tmp/rscala_1.0.6.tar.gz
    R -e "install.packages('ggplot2', repos = 'http://cran.us.r-project.org')"
    R -e install.packages('knitr', repos = 'http://cran.us.r-project.org')
    ```
   
    - Build + launch Zeppelin and test the R note.
   
    !!! you need rscala_1.0.6 (if not, you need to build with -Drscala.version=...)
   
    ### Screenshots (if appropriate)
   
    #### Simple R
   
    [![Simple R](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/simple-r.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/simple-r.png)
   
    #### Plot
   
    [![Plot](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/plot.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/plot.png)
   
    #### Scala R Binding
   
    [![Scala R Binding](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/scala-r.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/scala-r.png)
   
    #### R Scala Binding
   
    [![R Scala Binding](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/r-scala.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/r-scala.png)
   
    #### SparkR
   
    [![SparkR](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/sparkr.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/sparkr.png)
   
    ### Questions:
   
    * Does the licenses files need update? to be checked... (cfr R needs to be available to make this interpreter operational).
    * Is there breaking changes for older versions? No
    * Does this needs documentation? Yes


You can merge this pull request into a Git repository by running:

    $ git pull https://github.com/datalayer/zeppelin-R rscala-z

Alternatively you can review and apply these changes as the patch at:

    https://github.com/apache/incubator-zeppelin/pull/702.patch

To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:

    This closes #702
   
----
commit 363b2446fb01accee5e61e672e49cf152267b904
Author: Eric Charles <[hidden email]>
Date:   2015-11-20T13:01:47Z

    Add SparRInterpreter implementation

commit 9312a0ce109a8c73061ecef60cf7b3e1320368a2
Author: Eric Charles <[hidden email]>
Date:   2016-02-07T05:44:30Z

    Make rscala configurable in the spark-dependencies module

commit aa6a7a1ff9db48c999ef7c21465dd9a3d1c4d79a
Author: Eric Charles <[hidden email]>
Date:   2016-02-07T05:58:23Z

    Remove png files and restore README.md

----


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-180962488
 
    CLI fails for profiles 1.3, 1.2 and 1.1 with `object r is not a member of package org.apache.spark.api` which is normal as SparkR was introduced in 1.4.
   
    Profiles 1.4, 1.5 and 1.6 are green.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user Leemoonsoo commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181140583
 
    Thanks for the contribution.
   
    I think `spark/lib/rscala_2.10-1.0.6.jar` shouldn't be included in the source tree. Can this be downloaded on build time?
   
    And `rscala_2.10-1.0.6.jar` looks like available on BSD license according to [here](https://cran.r-project.org/web/packages/rscala/index.html). Then, you'll need add license of the library into `zeppelin-distribution/src/bin_license/LICENSE`, and add [LICENSE](https://cran.r-project.org/web/packages/rscala/LICENSE) file under `zeppelin-distribution/src/bin_license/licenses` directory.
   
    Most interpreters include at least one unittest or integration test. So I suggest have an test.
   
    I think R interpreter related source file need to be excluded for profile spark-1.3, spark-1.2, spark-1.1, so CI doesn't fail for those profile. I think maven capable of doing it.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user justsomeone1001 commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181147188
 
    I guess this isn't part of the 72-hour moratorium...
   
    @Leemoonsoo
   
    **Rscala**  Actually its not just that rscala *can* be downloaded at build time.  It *will* be downloaded whenever the user updates their R package library.  R data scientists users do quite regularly because the functionality is built into R.  There is no way to prevent an updated rscala from being used in place of the rscala included with this code.  (The issue is the R-side of the rscala library more than the java side, but that's beside the point.)
   
    This has already created breakages:  The author of rscala recently fixed a bug that affected Windows users.  The new version broke Eric's implementation, which had to be refactored.  
   
    **Licenses** Regarding licenses --you are correct that rscala is available under BSD. I convinced the author to switch from GPL to BSD so it could be used in PR 208.
   
    **Tests** You are astute to require unit tests.  The reason this code is passing CI is that it isn't being tested *at all.*  Neither R, nor the classes here, are ever executed.
   
    Related to that:  There's no code here to handle changes in the SparkInterpreter class, which has caused severe breakages in the spark-interpreter/R integration in the past.  There's also no code in here to handle the common Zeppelin/Spark misconfigurations that are 99% of the user issues that arise when you add R to zeppelin; or to handle spark-related issues at all.
   
    One reason for this is, surely, because Eric only added the integration a few weeks ago, after I pointed-out on the mailing list that the functionality was absent.  Since Eric based his code on mine (which he is absolutely entitled to do), I'm pretty sure it will start to have the same issues if it ever develops a user base.  
   
    **Other** There are a slew of other issues here related to integration with the rest of Zeppelin, presentation of R in a manner that R-using data scientists will be familiar with, and allowing the full R functionality.  
   
    As just one example:   it doesn't support R base-plotting, and I'm pretty sure it won't support interactive visualizations either.
   
    I am not going to list all of those issues here now, when we're trying to resolve the issue of PR 208 -- which *does* handle all of them, and quite a few more.  This is because I worked through them over the last six months in responding to requests and issues from users.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user hsaputra commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181199091
 
    @echarles Looks like this PR was trying to just add support for SparkR package.
    AFAIK this can be addressed #208 PR, can't it?


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181417475
 
    @Leemoonsoo
    - rscala is now downloaded at build time
    - bin_license updated
    - Unit test added
    - spark-1.3, spark-1.2, spark-1.1 should now build with maven machinery
   
    @justsomeone1001
    - This PR support visualization.
    - I have added a very first inistial documentation to help the setup.
   
    @hsaputra
    - Once you get SparR, you have R (just like PySpark, you get Python)
    - I have opened this PR to take into acocunt with my comments on #208 PR (see [1] and [2])
   
    [1] http://mail-archives.apache.org/mod_mbox/incubator-zeppelin-dev/201512.mbox/%3C5683E471.9010001%40apache.org%3E
    [2] https://github.com/apache/incubator-zeppelin/pull/208#issuecomment-170337289
   
    Thx for your comments so far and looking what Travis will tell...



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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user justsomeone1001 commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181463479
 
    @echarles It doesn't support base plotting.  Do you have an example of code to show that it supports *interactive* visualizations?  I believer it does not.
   
    Regarding @hsaputra 's comment -- your comment on 208 was that you didn't think R supported needed to have functionality that is in 208 but is not in this PR.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user smartinsightsfromdata commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181561671
 
    @echarles @justsomeone1001 could you kindly clarify if **native visualization** refers to **Zeppelin visualisations** or R?
   
    Visualisation is most relevant around data exploration and analytics results sharing (where notebooks make most sense). I think for R and Python users it would be good to know which visualisation will work out-of-the-box.  It could help to decide which tool / interpreter / language to use:
   
    1. Zeppelin native?
    2. language native (e.g. R core graphics `plot` etc.)?
    3. dedicated libraries (Python: matplotlib [w or w/o `%matplotlib inline` like jupyter?]; bokeh; R: ggplot2 etc.)
    4. interactive visualization (R: htmlwidgets;  relevant visualisations in Bokeh)



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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181565303
 
    2 failures on last build:
    spark-1.3: ZeppelinIT.testSparkInterpreterDependencyLoading:229->AbstractZeppelinIT.waitForParagraph:66->AbstractZeppelinIT.pollingWait:92 » Timeout
   
    spark-1.5  ZeppelinIT.testAngularDisplay:151 » NoSuchElement Unable to locate element: {"...
   
    The good news is that the SparkR related build and test are ok for all profiles.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181568340
 
    @echarles @justsomeone1001  This PR supports ggplot2 and displaying R dataframe in native zeppelin widget
   
    ## ggplot2
   
    [![Plot](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/plot.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/plot.png)
   
    ## dataframe in native zeppelin widget
   
    [![Interactive Plot](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/plot-interactive.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/plot-interactive.png)
   
    The best would be to start a thread on the Zeppelin development list to talk about further development and requirement.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user justsomeone1001 commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-181571398
 
    @echarles You could simply have answered him "no, this PR doesn't support R visualizations."  
   
    I am disinclined to start a thread.  I feel like by pointing out the features that your implementation is missing but are present in mine, I'm just helping you compete.  
   
    There isn't any benefit to the project from doing that, since what you've built is a subset of what's already in PR 208 and the revision on git.
   
    As you know, there's a moratorium on discussions about PR 208, which is what you based this one on.  I, for one, am happy for the break.  Perhaps you could consider respecting the moratorium for a few days?


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user Leemoonsoo commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182177214
 
    Moratorium on discussion about PR 208 is over (a day ago), and it was for only me and Amos.
    Zeppelin community never blocks discussion without good reason.
   
    So anyone feel free to comment in this PR.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182615851
 
    Last commit brings the ability to define the ggplot2 image size as asked on https://github.com/datalayer/zeppelin-R/issues/2
   
    I have also added more samples on interactive visualization.
   
    [![ggplot2](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/ggplot2.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/ggplot2.png)
   
    [![rcharts](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/rcharts.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/rcharts.png)
   
    [![maps](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/rcharts-map.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/rcharts-map.png)
   
    [![googlevis](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/googlevis.png)](https://raw.githubusercontent.com/datalayer/zeppelin-R/rscala/_Rimg/googlevis.png)



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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182617569
 
    Travis fails with
   
    ```
    Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.471 sec <<< FAILURE! - in org.apache.zeppelin.spark.SparkRInterpreterTest
    testSuccess(org.apache.zeppelin.spark.SparkRInterpreterTest)  Time elapsed: 0.496 sec  <<< ERROR!
    java.lang.ExceptionInInitializerError: null
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:186)
    at java.lang.ProcessImpl.start(ProcessImpl.java:130)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
    at scala.sys.process.ProcessBuilderImpl$Simple.run(ProcessBuilderImpl.scala:68)
    at org.ddahl.rscala.callback.RClient$.apply(RClient.scala:689)
    at org.ddahl.rscala.callback.RClient$.apply(RClient.scala:672)
    at org.apache.zeppelin.spark.ZeppelinR$.<init>(ZeppelinR.scala:40)
    at org.apache.zeppelin.spark.ZeppelinR$.<clinit>(ZeppelinR.scala)
    at org.apache.zeppelin.spark.ZeppelinR.css(ZeppelinR.scala)
    at org.apache.zeppelin.spark.SparkRInterpreter.format(SparkRInterpreter.java:179)
    at org.apache.zeppelin.spark.SparkRInterpreter.interpret(SparkRInterpreter.java:134)
    at org.apache.zeppelin.spark.SparkRInterpreterTest.testSuccess(SparkRInterpreterTest.java:83)
    ```
    Strangely, it was able to pass at least one time 2 days ago.
    I will double check on a platform that does not have R and mock more if needed.



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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user doanduyhai commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182632704
 
    Ohh my god, those charts are very sexy!


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user justsomeone1001 commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182638534
 
    @doanduyhai  https://github.com/elbamos/Zeppelin-With-R


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user doanduyhai commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182639390
 
    Those graphs in your repo are sexy too !
   
    To be honest, I'm comparing them to the current graph options that exist in standard Zeppelin (I'm not talking about custom code to have custom graphs) and those showed by R interpreter are nice.
   
     But I'm not qualified to judge about the quality of the R interpreter or whatsoever


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user justsomeone1001 commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182646344
 
    @doanduyhai If you pull the one from my repo, it includes a demo notebook with a whole slew of them.  The purpose of it is to give reviewers something so they understand the functionality.  Some of the charts will look familiar.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-182836577
 
    Last commit made the build successful for 4 the 5 profiles.
   
    The failing one is https://s3.amazonaws.com/archive.travis-ci.org/jobs/108515221/log.txt which claims `BUILD SUCCESSFULL` at the bottom of the page, and after `The command "./testing/startSparkCluster.sh $SPARK_VER $HADOOP_VER" failed and exited with 127 during `. I guess this is not the committed code but rather travis stability giving this.
   
    I have also opened https://issues.apache.org/jira/browse/ZEPPELIN-668 to get feedback on properties passing on paragraph run.


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[GitHub] incubator-zeppelin pull request: R and SparkR Support [WIP]

yx91490
In reply to this post by yx91490
Github user echarles commented on the pull request:

    https://github.com/apache/incubator-zeppelin/pull/702#issuecomment-183846468
 
    Build is now green.
   
    I am reorganizing my repos, and because github does not offer a way to change the repo/branch on a exisiting PR, I will close this one and reopen another one.


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