Linux3

Starting to administer systems

Introduction

This page is aimed at those moving from just being a Linux user to the role of a system administrator. Administering systems obviously requires more knowledge and also comes with more responsibilities.

A very common request from a user to an administrator is to add more software to a system. For this reason, we'll focus on the installation of packages in the next section.

Installing Software

Package Managers

• http://en.wikipedia.org/wiki/Package_management_system

YUM:

• http://en.wikipedia.org/wiki/Yellowdog_Updater,_Modified
• http://prefetch.net/articles/yum.html

APT:

• http://en.wikipedia.org/wiki/Advanced_Packaging_Tool
• https://help.ubuntu.com/community/AptGet/Howto

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.