Getting Started: Setting Up Rapache

In previous posts we've described how to set up CentOS running on a virtual machine in VirtualBox, and how to set up a standard LAMP configuration on that box.

The final pieces needed to run R with LAMP are:

• R built for use as a shared library
• rapache to connect R with Apache
• The "brew" package for processing HTML files with embedded R code
• Other packages we want to be available from R

Installing Dependencies

In order for Apache to load R, the R application needs to be built as a shared library.  As we are building R from the source, it's convenient to make sure we have installed other C libraries commonly needed by R first.

Recall that in the CentOS machine we configured there is a user "r-user" with password "r-passwd".  The system password is "r-lamp".  Start up CentOS and log in as "r-user".

Open a terminal and use the "su" command to gain administrative rights.  Then use "yum" to install the following packages:

yum install gcc-gfortran

yum install gcc-c++

yum install readline-devel

yum install libpng-devel libX11-devel libXt-devel

yum install texinfo-tex

yum install tetex-dvips

yum install docbook-utils-pdf

yum install cairo-devel

yum install java-1.6.0-openjdk-devel

yum install libxml2-devel

It isn't strictly required to install all of these.  For example, the "openjdk" libraries are only needed if the "rJava" package is going to be used.  However, it's much easier to install them all now than to rebuild R later when the desire to use "rJava" occurs.

Installing R

The first step is to retrieve the source "tar.gz" file from CRAN.  The source for the latest release is available from the main page of the CRAN web site, such as:

http://cran.r-project.org/src/base/R-2/R-2.10.1.tar.gz

Use Firefox to download this file, and move it to the home directory for "r-user".

At this point we need to follow the R installation instructions carefully.  Two important points:

• In order for the files to be readable by others, we need to set the appropriate default permissions for newly created files.  For example, set "umask 022".
• When configuring the R build, include the flag "--enable-R-shlib".

The following commands will unpack the files and build R 2.10.1, which is the most recent version when this was written:

umask 022

tar xf R-2.10.1.tar.gz

cd R-2.10.1

./configure --enable-R-shlib

make

For a quick check on whether R built correctly:

make check

When you are happy with the build, install R with:

make install

Installing R Packages

We will go ahead and install various packages that are likely to be of use with web applications.  It is likely that you will want to disallow installation of packages by R scripts run from Apache for security reasons, so the required packages would be installed in advance.

To install the packages, first use "cd" to change back to the home directory of "r-user" then start R with "R".  Package installation will possibly fail if you start "R" from within the directory where we were running the "make" command.

Use the "install.packages()" function to install the packages, such as:

install.packages(c("brew", "XML", "rjson", "RMySQL", "RJDBC", "rJava","Cairo", "Hmisc"))

The only package that's required for use with "rapache" is "brew".

Installing Rapache

The procedure for downloading, building, and installing Rapache is similar to that for R.  The main detail is you need to include "--with-apache2-apxs=/usr/sbin/apxs" when doing the configuration.

Download the "tar.gz" from the rapache web site:

http://rapache.net/files/rapache-1.1.9.tar.gz

Move the file to the home directory for "r-user" and run the following commands:

tar xf rapache-1.1.9.tar.gz

cd rapache-1.1.0

./configure --with-apache2-apxs=/usr/sbin/apxs

make install

Rapache is now installed.

Configuring Apache

The next step is configuring Apache HTTPD to load the R module.

Create a file "rapache.conf" in "/etc/httpd/conf.d" with this basic configuration information:

LoadModule R_module /etc/httpd/modules/mod_R.so

ROutputErrors

<Location /RApacheInfo>

  SetHandler r-info

</Location>

LoadModule tells Apache to load rapache.  ROutputErrors tells it to direct error messages from the R engine to the browser rather than just putting them in a log file.  SetHandler maps the "RApacheInfo" location to an action returning information about the rapache configuration.

To test this out, browse to "http://localhost/RApacheInfo".  Information about rapache should be displayed.

At this point we have rapache working, but Apache is not yet configured to process "R" or "RHTML" files.  That configuration and example test scripts will be covered in a later post.  If you are anxious to get that configuration in place, see the rapache manual for details.