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

[Steve Lianoglou]

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)

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