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
>>
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>>
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>>

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