Before you attempt to install bio3d you should have a relatively recent version of R installed and working on your system. Detailed instructions for obtaining and installing R on various platforms can be found on the R home page.


Obtaining bio3d


The bio3d package is distributed in two forms:

• as platform independent source code (download), VERSION 1.0-4 (MAY 2007)
• as a compiled binary for windows (download).

To install from source requires that your machine has standard compilers and tools such as Perl 5.004 or later. If you run into problems with source installation please refer to section 6.1 of the R Installation and Administration Manual.

For details of newly added features see the What'sNew wiki page.


Unix Installation


To install the bio3d package in a Unix enviroment download the source tar.gz file from above. At the shell command prompt type:

R CMD INSTALL bio3d_*.tar.gz

This will only work if you have permission to write files to the standard package installation location. If you would rather install to a different location you can set the R_LIBS enviroment variable to a location of your choice. For example, if you use tcsh then add a line similar to the following to your .tcshrc file:

setenv R_LIBS /net/home/bgrant/software/R/lib/R/library

Changing the path to a directory of your choice.


MacOS X Installation


R on Mac OS X can be used either on the command-line, like on other Unix systems, or via the R.app GUI. If you prefer to use the command line based R system then simply follow the Unix installation instructions above. Alternatively, you can use the Packages & Data menu of the GUI, in particular the sub-item Package Installer.
Download the source tar.gz file from above. In the R GUI select Packages & Data, Package Installer, Local Source Package and press the Install button. Select the bio3d tar file and press Open.


Windows Installation


To install the bio3d package on Windows download the compiled binary .zip file from above.
Start R and from GUI click Packages and then Install Package(s) from local zip file then simply select your downloaded bio3 zip file (something like bio3d_1.0-3.zip) and click Open to finish the installation. You should now be able to load the bio3d library into your current R session by typing the usual library(bio3d)command at the R Console.


Older Versions


Older versions of the package can also be obtained. Changes between versions are documented on the wiki along with a description of additional programs that may prove useful.


Where Next


For an introduction to working with bio3d and the R enviroment see the User Guide. A number of worked examples are available as short Tutorials on the bio3d wiki. You can also view the online Documentation.