[BioC] How to definitely point to local mirror?

Renaud Gaujoux renaud at mancala.cbio.uct.ac.za
Thu Nov 6 15:05:47 CET 2008


we've got a local mirror of Bioconductor (from version 2.1 to 2.3) and 
I'd like to know to do such that any request to the bioconductor 
repository (by any package) is actually send to our local mirror.
We setup a system-wide 'repos' options so that when a user do 
install.packages, the local mirror is included in the searched repositories.
- for example the GCRMA package (in 2.1 at least) seems to get its 
reposiroty URL from getOption('BioC'), which still point to bioconductor.org
- a call to Biobase::repoList() also returns bioconductor.org URLs

Is there a recommended way to change that so that the user doesn't have 
to car about the repositories, i.e. something that makes 
Biobase::repoList() returns our local mirror directories. Something to 
configure at the installation maybe, or override the function in the 
Rprofile.site file?

Obviously, if some packages have hard coded URLs then it won't work, but 
I guess this is part of the things that are checked before a package is 
actually included in the repository.


More information about the Bioconductor mailing list