[BioC] R and BioC package installation

Kasper Daniel Hansen k.hansen at biostat.ku.dk
Fri Apr 29 17:27:58 CEST 2005

Of the 16 members of R core, 5 are members of Bioconductor core. I do 
not think that you need to worry that there is no communication. Many 
changes in R in the last years have been initiated because of 
Bioonductor. And according to Seth (I have not yet looked at it myself), 
R's installation routines have been updated quite a bit in the new 
release. Probably at least partly inspired by Bioconductor.


On Fri, Apr 29, 2005 at 01:04:34PM +0200, Gregor GORJANC wrote:
> 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
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Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen

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