[Bioc-devel] adapting 'biocinstall' to my institute's needs

Seth Falcon sfalcon at fhcrc.org
Wed May 3 18:11:42 CEST 2006

Paul Shannon <pshannon at systemsbiology.org> writes:
> I have a number of R-shy users.  One big hurdle they face is installing
> packages.  'getBioC' and 'biocLite'  seem like just the right
> approach.

biocLite is trying to solve two problems:

1. Make it easy to install Bioc and/or CRAN packages and their
   dependencies.  To this end, it is really just a wrapper around
   install.packages that sets the repos option to a vector of Bioc
   package repositories (software, annotation, experiment, etc).

2. Choose the right collection of Bioc package repositories based on
   the version of R being used.

Florian pointed you towards the source.  If you plan to locally
support multiple R/Bioc versions then modifying these scripts seem
like a good way to go.  OTOH, if you can live with support for single
version, then you could simplify quite a bit --- that is, you just
need a wrapper on install.packages that lists all of your repositories
(and possibly points to internet repositories as well).

+ seth

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