[Bioc-devel] Custom CRAN repository in biocLite.R not working

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 at fhcrc.org>

On Wednesday, March 13, 2013, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

On Wednesday, March 13, 2013, Cristobal Fresno Rodr?guez
<cristobalfresno at 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

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