[BioC] Bioc packages not working with R2.15.2?

[Dan Tenenbaum]

On Fri, Nov 16, 2012 at 9:30 AM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Fri, Nov 16, 2012 at 12:11 PM, YBao <yb8d at virginia.edu> wrote:
>> Thanks to all who are helping with this matter.
>>
>> After doing what Dan suggested I am still getting an error:
>>
>>> options("BioC_mirror"="http://www.bioconductor.org")
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("RSQLite")
>> BioC_mirror: http://www.bioconductor.org
>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>> Installing package(s) 'RSQLite'
>> Warning: unable to access index for repository
>> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib
>> Warning: unable to access index for repository
>> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.15
>> Warning: unable to access index for repository
>> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.15
>> Warning message:
>> package ‘RSQLite’ is not available (for R version 2.15.2)
>

Sorry, I guess you need to change your CRAN mirror.
Try this:
chooseCRANmirror()
and pick one of the ones I know is good: Switzerland or USA (WA 1).

But yes, starting over would probably be good. And as suggested, using
R --vanilla

Dan



> This is quite strange. I just entered the same exact commands and it
> works for me (also running R-2.15.2 on osx).
>
> I'm a bit confused, though, why even after you set your bioc mirror,
> you are still trying to get your packages from `...harvard.edu`.
>
> I guess your problem lies there.
>
>> Would it be advisable to clean up everything related to R and BioC then
>> reload everything fresh?
>
> I suspect that's easy enough to try.
>
> The only other thing I can suggest for debugging purposes is to start
> R (via terminal) w/ the --vanilla switch, in case some setting/thing
> somewhere is tripping you up, eg. form the shel:
>
> $ R --vanilla
> R> options("BioC_mirror"="http://www.bioconductor.org")
> R> source("http://bioconductor.org/biocLite.R")
> R> biocLite("RSQLite")
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact