Dear Dan

The solution you suggested did the trick. In addition I also tried

options("repos" = c(CRAN="http://mycranmirror"))

which successfully did the trick in changing biocinstallRepos() output. I
would suggest to modify biocLite comment from

## options("repos" = "http://cran.fhcrc.org")

to

## options("repos" = c(CRAN="http://cran.fhcrc.org"))

Thanks for the assistance.


Kachelo











2013/3/13 Dan Tenenbaum <dtenenba@fhcrc.org>

>
>
> On Wednesday, March 13, 2013, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
> >
> >
> > 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")
> Er, this should be:
> repos <- getOption("CRAN")
>
>
> > repos["CRAN"] <- "http://mycranmirror"
> > options(repos=repos)
> >
> > Then check the value of
> > biocinstallRepos()
> >
> > Dan
> >>
> >> Best regards
> >>
> >> Kachelo
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>

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