Linux3

Starting to administer systems =Introduction=

=Installing Software=

Building from Source Code
Let's build the latest and greatest version of the popular, open-source statistics package--R. We can download the source code from a mirror site right here in Bristol!

cd $HOME mkdir BUILD mkdir INSTALL cd BUILD mkdir R cd R wget http://www.stats.bris.ac.uk/R/src/base/R-3/R-3.0.1.tar.gz

OK, take a look at what we have so far:

ls -l -rw-r--r-- 1 gethin gethin 25508280 2013-05-16 08:11 R-3.0.1.tar.gz

So far, so good. Let's unpack the tarball:

tar -xzf R-3.0.1.tar.gz ls -l drwxr-xr-x 10 gethin gethin    4096 2013-05-16 08:11 R-3.0.1 -rw-r--r-- 1 gethin gethin 25508280 2013-05-16 08:11 R-3.0.1.tar.gz

We have a directory called R-3.0.1, let's move into that directory and take a look at what's inside:

cd R-3.0.1 ls ChangeLog   configure     COPYING  etc      m4           Makefile.fw  NEWS      ONEWS   po      share  SVN-REVISION  tools    VERSION-NICK config.site configure.ac  doc      INSTALL  Makeconf.in  Makefile.in  NEWS.pdf  OONEWS  README  src    tests         VERSION

It's common to find files named README and INSTALL, which will give details of the project and installation instructions, respectively.

In common with many other projects, the R distribution uses something called the automake package which creates makefiles for subsequent use in compiling the source code. The typical pattern of commands in this situation is to run ./configure, followed by make, possibly some sort of test, and finally make install to complete the software installation.

Configure scripts often follow convention when it comes to the options that they will accept. For example:

./configure --help

will list all the valid options for this particular configure script. --prefix is a common option. We can use it to tell the system where we would ultimately like the package to be installed, once it is built. For the purposes of this example, we will run:

./configure --prefix=$HOME/INSTALLS/R/3.0.1

This command will spew a great deal of information to the screen. For less forgiving configure scripts, you'll need eyes like a hawk to spot signs of a configuration problem as the results of interrogating the system scroll past. Happily in this case, however, the configure script gives us a handy summary at the end:

R is now configured for i686-pc-linux-gnu

Source directory:. Installation directory:   /home/gethin/INSTALLS/R/3.0.1

C compiler:               gcc -std=gnu99  -g -O2 Fortran 77 compiler:      gfortran  -g -O2

C++ compiler:             g++  -g -O2 Fortran 90/95 compiler:   gfortran -g -O2 Obj-C compiler:

Interfaces supported:     X11 External libraries:       readline Additional capabilities:  PNG, JPEG, NLS Options enabled:          shared BLAS, R profiling

Recommended packages:     yes

Now we're in the position to start compiling-up the source code. To do this, run make:

make

At this point, you'll see a good deal more information regarding the compilation scroll over your terminal too. The R build adds in some helpful commentary, so that it is not too cryptic. If you have been able to build without any errors, you can check that the package is behaving correctly by running:

make check

All being well, you should see many OKs scroll past.

Finally, when you are satisfied that all is well, you can install the package at it's intended destination:

make install

We can check that it installed correctly by looking in under the directory specified to the configure script via the --prefix option:

ls $HOME/INSTALLS/R/3.0.1 bin lib  share ls $HOME/INSTALLS/R/3.0.1/bin R Rscript

Finally, you can start the package by typing $HOME/INSTALLS/R/3.0.1/bin/R (where, for convenience, you will want to add this bin directory to your path. ):

$HOME/INSTALLS/R/3.0.1/bin/R R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: i686-pc-linux-gnu (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.

>

R has a neat graphics demo facility that you can start by typing:

demo(graphics)

Congratulations! You've successfully downloaded, built and installed the R package from source code. This will stand you in good stead for installing other packages and tools.