On Wednesday, March 13, 2013, Cristobal Fresno Rodríguez <
cristobalfresno@gmail.com> wrote:
> 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?
>

Try:
repos <- get option("repos")
repos["CRAN"] <- "http://mycranmirror"
options(repos=repos)

Then check the value of
biocinstallRepos()

Dan
>
> Best regards
>
> Kachelo
>
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