[BioC] Chromosome view of Nimblegen data

James W. MacDonald jmacdon at med.umich.edu
Fri Dec 15 15:21:37 CET 2006

Hi Jose,

J.delasHeras at ed.ac.uk wrote:

> I downloaded the .gz file, and uncompressed it with 7zip. The  
> resulting .tar file is nothing that I seem to be able to deal with  
> from the RGui menu, so I uncompressed it again to give a folder called  
> 'chIPchip', containing sevral other folders. Then I compressed it into  
> a .zip file, and tried to install it from the menu (install package  
> from local zip files). That proceeds without errors, but then:
> Error in library(chIPchip) : 'chIPchip' is not a valid package --  
> installed < 2.0.0?
> I am sure you're laughing at my naivety thinking that this roundabout  
> would work, but I just don't know what else I could do, other than  
> getting a Mac? :)
> Is there any way to install the package to run on a WinXP system?

Not surprisingly, this is a fairly common thing for people to attempt. 
In the past, for packages that contained only R code, you could do 
something quite similar and have it work. But no longer.

To install a source package on windows, you need to install some 
software on your computer and do some other things to get set up. 
Instructions for doing so can be found here:


Note that you don't need to do everything on that page (it is primarily 
designed to show how to build R itself on windows), but you do need 
everything up to 'Building R Itself', except for the part about 
Cross-compilers. I would recommend installing the Microsoft HTML Help 
Workshop because it is easy to do, and it's a pain to remember to not 
build chm help files.

You might also install MiKTeX, so you can build vignettes, etc. This is 
a simple process, but the installer takes some time because of all the 
little packages it has to download and install.

Also, the instructions on that page are quite terse (welcome to R ;-D), 
so it is important to follow exactly what they say, and to ensure you 
understand what they mean.

Have fun!



> thanks!
> Jose
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United  
> Kingdom.1252;LC_MONETARY=English_United  
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
> other attached packages:
>    limma
> "2.9.1"

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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