[BioC] R and BioC package installation

Seth Falcon sfalcon at fhcrc.org
Thu Apr 28 16:12:01 CEST 2005

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

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.  

+ seth

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