[BioC] Re: [R] Source package installation for WinXPpro

James MacDonald jmacdon at med.umich.edu
Thu Oct 9 08:47:35 MEST 2003

You need to make sure that all the tools are in your path, with the R
tools before perl and mingw. Set this by right clicking My Computer,
then properties, advanced, environment variables, then edit the path in
the system variables window. Once you have done that, you should be able
to download the sources (put them in a folder where the path doesn't
contain spaces. In addition, it is best if R is in a path that doesn't
contain spaces (so C:\Program Files\Rw1080 is not ideal. I usually
install in C:\Rw1080, but do what you like.)

Next, open a command prompt. Start menu, run, type cmd, enter. Then cd
to the folder where the affy.tar.gz resides and type 'tar xvfz affy*gz'
without the quotes. After everything is untarred and unzipped, cd to
Rw1080\bin and type 'rcmd install <path to affy folder>'. Windows is
case insensitive (mostly), so you don't need to capitalize. You should
then see a bunch of stuff happening, hopefully none of which contains an
error message.

If something doesn't work, re-read Brian Ripley's page on compiling. You
can also get good information by downloading the R-1.8.1 tarball and
looking for the readme-packages file.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> <Phguardiol at aol.com> 10/09/03 06:53 AM >>>
I d like to compile the source code from last Affy package for WinXPpro
however the doc is pretty poor regarding this process...
I went to FAQ R Win then to http://www.stats.ox.ac.uk/pub/Rtools/ and 
downloaded in The essentials, tools and Perl 5.8.0, then MingW from
www.mingw.org and 
I wonder if I need any other stuff from this page ? I m not sure but I
think I need the cross-conpilers ? what about the others below ? Then I 
installed MingW and Perl.
Then what am i suposed to do....?
If I click on Rcmd I dont get any windows to open or just for a
thanks for your help

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