[BioC] R and BioC package installation

Gregor GORJANC gregor.gorjanc at bfro.uni-lj.si
Thu Apr 28 16:31:37 CEST 2005

James W. MacDonald wrote:
> 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.
Jim, >

Jim, thanks for the response. But that would also be usable for "pure R". 
Why wasn't this just merged together.

Lep pozdrav / With regards,
     Gregor Gorjanc

University of Ljubljana
Biotechnical Faculty        URI: http://www.bfro.uni-lj.si/MR/ggorjan
Zootechnical Department     mail: gregor.gorjanc <at> bfro.uni-lj.si
Groblje 3                   tel: +386 (0)1 72 17 861
SI-1230 Domzale             fax: +386 (0)1 72 17 888
Slovenia, Europe
"One must learn by doing the thing; for though you think you know it,
  you have no certainty until you try." Sophocles ~ 450 B.C.

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