Tag Archives: raspberrypi

R Tutorials

How to Install the Latest Version of R Statistics on Your Raspberry Pi

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R for Beginners:  How to Install the Latest Version of R Statistics on Your Raspberry Pi

A tutorial by D. M. Wiig

One of the nice characteristics of open source software such as R is the rapid development of new releases and updates.  While the base core remains stable for a period of time there is a considerable amount of updating,  adding, and removing the component packages.  At the time of this writing the latest iteration is R version 3.3.1, “Bug in Your Hair.” If you are using a Windows platform you will likely go directly to the archive web site and download the latest distribution as a Windows executable installation package.

If you are using a Linux distribution  such as Ubuntu or Debian, the process of adding software is usually accomplished via the menu based installer.  These software installers allow  R and its dependencies to be downloaded from the community archive.

One of the disadvantages of using this approach is that the versions of some software in the community archives may not be updated to the latest version.  This is often the case with R as well as with many other software packages.

To insure that you are downloading the latest R version you need to use the platform’s command line to install what is needed.  You can add the URL’s of some backport archives that are more likely to be kept up to date with current releases.  As an example In this tutorial I will use the R statistical software that I am running on my Raspberry Pi 3 board with a Raspbian OS and the new PIXEL desktop.

Regardless of which Linux distribution you are using first open a command console from the desktop menu. Make sure all is up to date by using the command:

pi@raspberrypi:~ $ sudo apt-get update
This will insure all appropriate packages currently installed are running the latest updates.  If you are running a Raspbian distribution such as jessie you will need to edit the /etc/apt/sources.list file to add a backport to the latest version of R.  Start the nano editor by using the command:

sudo nano /etc/apt/sources.list

This should produce the output as seen below:

pi@raspberrypi:~ $ sudo nano /etc/apt/sources.list

------------------------------------------------
GNU nano 2.2.6 File: /etc/apt/sources.list

deb http://mirrordirector.raspbian.org/raspbian/ jessie main contrib non-free r$
# Uncomment line below then 'apt-get update' to enable 'apt-get source'
deb-src http://archive.raspbian.org/raspbian/ jessie main contrib non-free rpi
deb http://archive.raspbian.org/raspbian/ stretch main
deb http://mirror.las.iastate.edu/CRAN/bin/linux/debian/ jessie main
deb http://mirror.las.iastate.edu/CRAN/bin/linux/ubuntu xenial/

[ Read 8 lines ]
^G Get Help ^O WriteOut ^R Read File ^Y Prev Page ^K Cut Text ^C Cur Pos
^X Exit ^J Justify ^W Where Is ^V Next Page ^U UnCut Text^T To Spell

As is seen above there are several lines containing the standard  Raspbian archives to search.

If you are using a Debian distribution you would add the following line to the file:

http://mirror.las.iastate.edu/CRAN/bin/linux/debian/ jessie main

Replace the 'jessie' portion with the name of the specific Debian distribution you are using replace the 'mirror' portion with the R CRAN mirror that you use.  You also need to add the line that provides the URL of a Raspian 'stretch' archive that contains the most recent updates of many different software packages.  In my case I was looking for the latest R release, but you should search this this archive for the latest version of any software package you are installing.

If you are using an Ubuntu distribution add a line with the appropriate changes for the specific Ubuntu distribution that you are using. 
Check with the documentation provided with your specific Linux distribution to see if there is also a 'stretch' archive maintained for new versions. 

Once these changes are made exit the nano editor using the ^O key command to write the file and then the ^X key command to return to the command line.  You should now be able to issue the command:

pi@raspberrypi:~ $ sudo apt-get install r-base r-base-core r-base-dev

Once the download and install processes have completed you should now be able to invoke R from the command line or menu and see the latest version:

pi@raspberrypi:~ $ R

R version 3.3.2 RC (2016-10-23 r71578) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: arm-unknown-linux-gnueabihf (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

 Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 


For other Linux distributions you would add a line similar to the above examples in the /etc/apt/sources.list. Check the documentation for your specific Linux platform for further information about backport archives.
Book Reviews

Book Review: Raspberry Pi Super Cluster

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Andrew K. Dennis. Raspberry Pi Super Cluster. Birmingham, England: PACKT Publishing, 2013.

A book review by D.M. Wiig

In the computer world clusters and supercomputers are used for some of the most demanding and complex tasks facing todays technology. Raspberry Pi Super Cluster by Andrew Dennis is a recently published work that demonstrates how this technology can be explored right in your own home or in the classroom using modest, inexpensive hardware and readily available free open source software.

This book is a well written and easy to understand introduction to the theory and practice of parallel computing that is suitable for hobbyists, educators or others who what to explore this interesting facet of computing. The widespread availability and low price of the Raspberry Pi computer makes building a real parallel computing cluster available for anyone who is interested in exploring this topic. In order to get the most from this book the reader should have some experience in working with computers and programming languages. A knowledge of the concepts involved in parallel and cluster computing is not required as the author covers the basics of these topics quite thoroughly. Some knowledge of working with the Raspberry Pi the Linux command line interface is also desirable.

The author starts out in chapter one with a discussion of some of the basic concepts involved in parallel computing such as supercomputers, multi-core and multi-processor machines, and cloud computing. Central to this introduction is the concept of commodity hardware clusters. The concept of using these groups of commodity off-the-shelf single board computers was pioneered in the late 1990’s and were know as Beowolf clusters, the name given to the concept of Network of Workstations (NOW) for scientific computing. The author concludes the introduction with a discussion of the Raspberry Pi computer which forms the basis of the computing cluster developed in the book. There is also a brief consideration of programming languages such as C, C++, and FORTRAN which are commonly used in Linux based computer clusters.

The author moves on to discuss in detail the hardware and software required to set up the cluster. Topics include setting up the Raspberry Pi, downloading and installing the Raspian operating system on an SD card and the initial setup of options such a SSH, the nano text editor, and installing the GCC FORTRAN compiler.

Chapter three of the book is devoted to the basics of setting up the foundation of a parallel computer interface with the MPI (Message Passing Interface) implementation. The book presents a step by step approach to downloading, installing, and configuring the MPICH software which is at the basis for the parallel computing environment. Once the system has been set up and tested on the first RPi the author turns to the task of setting up the second RPi that will be used in the configuration. It should be noted that the author provides abundant and detailed references to additional resources that the reader can access to assist in understanding or expanding upon the procedures discussed in the book. When the second RPi has been set up the author presents the design of a test program that will be used to check the installation, including detailed discussion of the code that is used. There is a nice feature of books published by PACKT that should be noted at this point. If the reader purchased the book from the publisher directly there is access to a download of all of the code that is presented in the book. This is a tremendous time saving feature and can help reduce coding mistakes that can lead to frustrating and hard to find errors.

While the first half of the book deals primarily with the installation and configuration of the RPi parallel cluster, the second half of the book deals with the application and development of distributed applications that will run on the RPi cluster. The author starts with a discussion of the technology known as Apache Hadoop, which is an open source project for developing distributed applications and is hosted by the Apache Software Foundation. The reader is then taken through the process of downloading and installing Java and the Java Development Kit, and downloading, installing, configuring, and testing the Hadoop server. Once again, there is a detailed and relatively easy to understand presentation of each step involved in the process. The author then turns to the setup of the second RPi, which is very similar to the setup for the first RPi. The second RPi setup tends to go faster as there is some duplication of configuration files.

The remaining chapters of the book are devoted to a presentation of some specific applications that can be run on the RPi cluster. There is a nice discussion of using the MapReduce programming approach on the RPi cluster. MapReduce is a programming approach that allows systems to process large datasets in parallel. The author takes the reader through an overview of the WordCount MapReduce program and a step by step testing of this program on the RPi cluster. There is also a chapter devoted to Monte Carlo simulators, which use large data sets and randomized sampling repeatedly in order to obtain a result for a particular mathematical question. The reader is walked through an example of using this technique on the RPi cluster to calculate Pi. The last chapter of the book explores other topics relating the the RPi cluster such as adding external USB disk drive for greater storage capacity and installing and experimenting with the FORTAN programming language on the cluster.

I found this book to be interesting, informative and challenging. It stimulated my interest in furthering my knowledge of cluster computing and the potential of the Raspberry Pi computer in that endeavor. I am a big fan of open source projects and I currently own two RPi’s. One is being used as a dedicated web server that hosts my WordPress Raspberry Pi and R statistics web site. The other is for experimental purposes. After reviewing this book I am planning to add a third (or fourth) RPi to my collection so that I can experiment with parallel computing. I recommend this book to computer users at all levels. It will help you in reading the book if you have some experience with computer hardware, operating systems, and programming languages, but for those less knowledgeable readers the author provides abundant links to additional information, source code and other sources that make this a good read for those with less hands on experience.

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Author Information: Douglas M. Wiig

I am a Professor of Political Science at Grand View University in Des Moines, Iowa, USA. My teaching areas of expertise include social science statistics, social science research methods, comparative and international politics. I am also interested in developing methods to integrate technology into the university curriculum. I have used computers, and various programming languages in the classroom, in academic research and writing an in personal projects since the days when data and programming instructions where entered into mainframe behemoths on punched cards and personal computing platforms were still a dream. I am a big fan of open source projects and contribute whatever I can to the continuing growth and success of the community.

Contact Information: Douglas M. Wiig

Email: dwiig@grandview.edu dmartin6412@gmail.com

Web Site/Blog: http://raspberrypiandr.net

 

Book Reviews

Book Review: Raspberry Pi Super Cluster

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Book Review: Piotr J. Kula. Raspberry Pi Server Essentials. Birmingham, UK: Packt Publishing, 2014.

 A book review by D.M. Wiig

Raspberry Pi Server Essentials is an informative, step by step discussion of how this amazing little computer can be set up as a fully functioning web server. The book begins with a discussion of the basics of setting up a Raspberry Pi and walks the reader through the process of obtaining necessary hardware, installation of the Raspian operating system and initial system configuration. There is also a brief discussion of the design of the Raspberry Pi for readers who are more technically inclined.

I might point out that if the reader is not comfortable working at the command line level and performing system operations such as disk formatting and writing or directory tasks that this section may be a little daunting. Less technically inclined readers may want to purchase an SD card that is preloaded with the Raspberry Pi operating system software. These cards are available from a number of sources at a reasonable price and provide plug-and-play convenience.

After discussing the Raspberry Pi hardware setup the author moves to a consideration of network configuration from Local Area Networks to wireless and Ethernet connections. Once again there is a concise presentation of some of the basics for readers who have some experience working with routers and home networks. After a discussion of performing Raspberry Pi system updates and some basic system monitoring functions the author turns to the task of installing a web server on the Raspberry Pi.

There are several good open source web servers available for Linux operating systems such as Apache software, but the author points out that while these servers contain a number of useful features and are very powerful they are also cumbersome when used on a computer with limited RAM and a relatively slow processor such as the Raspberry Pi. The use of a fast PHP based web server called nginx (pronounced ‘engine x’) is one solution to this problem. Nginx is a fast lightweight server that is designed to deliver the maximum content with a minimum load on system resources. The author first walks the reader through a discussion of downloading and installing nginx. There is also a discussion of downloading and setting up a lightweight SQL database server called SQLite3 to run on the server.

The remaining chapters of the book discuss how to set up and use a number of useful applications on your now functioning Raspberry Pi web server. These applications include setting up and managing a file server, using the Raspberry Pi as a game server for popular open source games such as OpenTTD, using the official HD camera module designed by the Raspberry Pi Foundation for streaming live HD video, and setting up the Raspberry Pi to control a home media center.

There is also an interesting discussion of setting up software on the Raspberry Pi for use with the Bitcoin cryptocurrency implementation. Readers are walked through the installation of Bitcoin software bitcoind on the Raspberry Pi and the use of Bitcoin wallets and Bitcoin web addresses. The chapter concludes with a brief section on Bitcoin mining with CGMiner software.

Raspberry Pi Server Essentials is a concise yet informative look at how the Raspberry Pi can be used in a variety of web server applications. Some technical knowledge of basic hardware and command level interaction with the operating system software is helpful in reading this book but not essential. For those readers who desire more information the author provides a number of links to additional resources pertaining to the material covered in each chapter. The world of open source technology is an amazing one. This book is a good read for those who want to venture into managing their own open source based web server.

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