[BioC] R and BioC package installation

[James W. MacDonald]

Gregor GORJANC wrote:
> Hello!
> 
> Can someone point me to explanation/documentation why Bioconductor uses 
> also some other "package installation" design in contrast to R. I 
> appologize for ignorance, but I am just starting with Bioconductor and 
> was surprised on this difference to pure R.
> 
I think there are at least two reasons. First, the reposTools/getBioC 
paradigm allows one to specify a 'theme' of packages to download, based 
on the sort of analyses one might be interested in performing. For 
instance, getBioC("affy") will get all the packages you will likely need 
to use for Affymetrix chip analyses. AFAIK, there is no such 
functionality in the standard install.packages(). Instead, you have to 
seek out the packages you want to install from CRAN.

Second, rather than having all the packages in one big repository (a la 
CRAN), the BioC repositories are separated out by function or type, so 
installing a set of packages may require iteration through 11 different 
repositories in order to get all the requested packages. I don't believe 
that this was easy to do with the base installation functionality when 
Bioconductor was first started.

Best,

Jim



-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623