Greetings!!

I am trying to use a local CRAN and Bioconductor repository for
academic purposes. In this context, in biocLite.R  script at
bioconductor.org suggests to use:

options("repos" = "http://localCRANsite")

options("BioC_mirror" = "http://localBioconductorSite")

source("http://bioconductor.org/biocLite.R")

biocLite("package name").

After applying this modifications, only packages dependencies from
Bioconductor will user the local http://localBioconductorSite
repository. But, CRAN dependencies will override new "repos" value and
use http://cran.fhcrc.org instead. However, any
install.packages("package whatever") uses the new local repository
link.

I believe the problem lies in biocinstallRepos() function as it
returns a name character where CRAN value is "http://cran.fhcrc.org"
instead of the new link. Digging a little more, this function calls
.biocinstallRepos which has hard-coded inside "http://cran.fhcrc.org".

Can someone has a workaround?


Best regards

Kachelo

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