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| |
| <h1>R Interpreter for Apache Zeppelin</h1> |
| |
| <div id="toc"></div> |
| |
| <h2>Overview</h2> |
| |
| <p><a href="https://www.r-project.org">R</a> is a free software environment for statistical computing and graphics.</p> |
| |
| <p>To run R code and visualize plots in Apache Zeppelin, you will need R on your master node (or your dev laptop).</p> |
| |
| <ul> |
| <li>For Centos: <code>yum install R R-devel libcurl-devel openssl-devel</code></li> |
| <li>For Ubuntu: <code>apt-get install r-base</code></li> |
| </ul> |
| |
| <p>Validate your installation with a simple R command:</p> |
| <div class="highlight"><pre><code class="text language-text" data-lang="text">R -e "print(1+1)" |
| </code></pre></div> |
| <p>To enjoy plots, install additional libraries with:</p> |
| <div class="highlight"><pre><code class="text language-text" data-lang="text">+ devtools with `R -e "install.packages('devtools', repos = 'http://cran.us.r-project.org')"` |
| + knitr with `R -e "install.packages('knitr', repos = 'http://cran.us.r-project.org')"` |
| + ggplot2 with `R -e "install.packages('ggplot2', repos = 'http://cran.us.r-project.org')"` |
| + Other vizualisation librairies: `R -e "install.packages(c('devtools','mplot', 'googleVis'), repos = 'http://cran.us.r-project.org'); require(devtools); install_github('ramnathv/rCharts')"` |
| </code></pre></div> |
| <p>We recommend you to also install the following optional R libraries for happy data analytics:</p> |
| |
| <ul> |
| <li>glmnet</li> |
| <li>pROC</li> |
| <li>data.table</li> |
| <li>caret</li> |
| <li>sqldf</li> |
| <li>wordcloud</li> |
| </ul> |
| |
| <h2>Configuration</h2> |
| |
| <p>To run Zeppelin with the R Interpreter, the <code>SPARK_HOME</code> environment variable must be set. The best way to do this is by editing <code>conf/zeppelin-env.sh</code>. |
| If it is not set, the R Interpreter will not be able to interface with Spark.</p> |
| |
| <p>You should also copy <code>conf/zeppelin-site.xml.template</code> to <code>conf/zeppelin-site.xml</code>. That will ensure that Zeppelin sees the R Interpreter the first time it starts up.</p> |
| |
| <h2>Using the R Interpreter</h2> |
| |
| <p>By default, the R Interpreter appears as two Zeppelin Interpreters, <code>%r</code> and <code>%knitr</code>.</p> |
| |
| <p><code>%r</code> will behave like an ordinary REPL. You can execute commands as in the CLI. </p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/repl2plus2.png" width="700px"/></p> |
| |
| <p>R base plotting is fully supported</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/replhist.png" width="550px"/></p> |
| |
| <p>If you return a data.frame, Zeppelin will attempt to display it using Zeppelin's built-in visualizations.</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/replhead.png" width="550px"/></p> |
| |
| <p><code>%knitr</code> interfaces directly against <code>knitr</code>, with chunk options on the first line:</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/knitgeo.png" width="550px"/></p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/knitstock.png" width="550px"/></p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/knitmotion.png" width="550px"/></p> |
| |
| <p>The two interpreters share the same environment. If you define a variable from <code>%r</code>, it will be within-scope if you then make a call using <code>knitr</code>.</p> |
| |
| <h2>Using SparkR & Moving Between Languages</h2> |
| |
| <p>If <code>SPARK_HOME</code> is set, the <code>SparkR</code> package will be loaded automatically:</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/sparkrfaithful.png" width="550px"/></p> |
| |
| <p>The Spark Context and SQL Context are created and injected into the local environment automatically as <code>sc</code> and <code>sql</code>.</p> |
| |
| <p>The same context are shared with the <code>%spark</code>, <code>%sql</code> and <code>%pyspark</code> interpreters:</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/backtoscala.png" width="700px"/></p> |
| |
| <p>You can also make an ordinary R variable accessible in scala and Python:</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/varr1.png" width="550px"/></p> |
| |
| <p>And vice versa:</p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/varscala.png" width="550px"/></p> |
| |
| <p><img class="img-responsive" src="../assets/themes/zeppelin/img/docs-img/varr2.png" width="550px"/></p> |
| |
| <h2>Caveats & Troubleshooting</h2> |
| |
| <ul> |
| <li><p>Almost all issues with the R interpreter turned out to be caused by an incorrectly set <code>SPARK_HOME</code>. The R interpreter must load a version of the <code>SparkR</code> package that matches the running version of Spark, and it does this by searching <code>SPARK_HOME</code>. If Zeppelin isn't configured to interface with Spark in <code>SPARK_HOME</code>, the R interpreter will not be able to connect to Spark.</p></li> |
| <li><p>The <code>knitr</code> environment is persistent. If you run a chunk from Zeppelin that changes a variable, then run the same chunk again, the variable has already been changed. Use immutable variables.</p></li> |
| <li><p>(Note that <code>%spark.r</code> and <code>%r</code> are two different ways of calling the same interpreter, as are <code>%spark.knitr</code> and <code>%knitr</code>. By default, Zeppelin puts the R interpreters in the <code>%spark.</code> Interpreter Group.</p></li> |
| <li><p>Using the <code>%r</code> interpreter, if you return a data.frame, HTML, or an image, it will dominate the result. So if you execute three commands, and one is <code>hist()</code>, all you will see is the histogram, not the results of the other commands. This is a Zeppelin limitation.</p></li> |
| <li><p>If you return a data.frame (for instance, from calling <code>head()</code>) from the <code>%spark.r</code> interpreter, it will be parsed by Zeppelin's built-in data visualization system. </p></li> |
| <li><p>Why <code>knitr</code> Instead of <code>rmarkdown</code>? Why no <code>htmlwidgets</code>? In order to support <code>htmlwidgets</code>, which has indirect dependencies, <code>rmarkdown</code> uses <code>pandoc</code>, which requires writing to and reading from disc. This makes it many times slower than <code>knitr</code>, which can operate entirely in RAM.</p></li> |
| <li><p>Why no <code>ggvis</code> or <code>shiny</code>? Supporting <code>shiny</code> would require integrating a reverse-proxy into Zeppelin, which is a task.</p></li> |
| <li><p>Max OS X & case-insensitive filesystem. If you try to install on a case-insensitive filesystem, which is the Mac OS X default, maven can unintentionally delete the install directory because <code>r</code> and <code>R</code> become the same subdirectory.</p></li> |
| <li><p>Error <code>unable to start device X11</code> with the repl interpreter. Check your shell login scripts to see if they are adjusting the <code>DISPLAY</code> environment variable. This is common on some operating systems as a workaround for ssh issues, but can interfere with R plotting.</p></li> |
| <li><p>akka Library Version or <code>TTransport</code> errors. This can happen if you try to run Zeppelin with a SPARK_HOME that has a version of Spark other than the one specified with <code>-Pspark-1.x</code> when Zeppelin was compiled.</p></li> |
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