[BioC] R and BioC package installation

Gregor GORJANC gregor.gorjanc at bfro.uni-lj.si
Fri Apr 29 13:04:34 CEST 2005

Seth thanks for clarification. Now I understand the "whole" thing. However, 
I would like to add a comment. Don't take me wrong. A appreciate very much 
work done by Bioconductor, R team and other volunteers. All of them are 
just doing marvelous job.

As I understand Seth's comments, Bioconductor developed new/improved 
package managing system, due to dependency issues. I understand that 
dependencies might be a bit more complicated than in R, but I'am sure that 
such improvements would be of much more benefit if they would also be used 
by "pure R". Therefore, improvements of R's related projects as 
Bioconductor and others should also find their way "back" into R. Finally, 
I realize that usually their is lack of people to do all this.

Thanks again and good luck!

> To follow up on James' comments, when Bioconductor started, R's
> install.packages and friends did not have a way of handling
> dependencies between packages.    
> Bioconductor was one of the first collections of packages that had a
> complicated/deep dependency structure.  In many ways this is a good
> thing as it demonstrates code reuse and collaboration.  The project
> had to "roll its own" package installation code in order to deal with
> the dependencies.
> In the latest release of R, the package installation tools have been
> vastly improved.  They are now capable of resolving dependencies
> between a collection of package repositories.  
> The Bioconductor team is evaluating to what extent we can utilize the
> new capabilities built into R and move away or adapt the reposTools
> code.
> I think we will continue to have an install script ala getBioC in
> order to simplify the process and provide some themed installs, as
> James mentioned. 
> Hope that helps a bit for some background.  

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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