[BioC] problem installing GenomicFeatures

[Steve Lianoglou]

Hi,

On Mon, Apr 29, 2013 at 9:23 AM, Kavita Garg [guest]
<guest at bioconductor.org> wrote:
>
> I am having trouble updating GenomicFeatures package. Can you please look at it and let me know what I doing wrong.
>
> this is the error I get
>
> Error : object ‘findSpliceOverlaps’ is not exported by 'namespace:GenomicRanges'
> ERROR: lazy loading failed for package ‘GenomicFeatures’
>
> thanks
> kavita
>
>> biocLite("GenomicFeatures")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.9.
> Installing package(s) 'GenomicFeatures'
> trying URL 'http://bioconductor.org/packages/2.10/bioc/src/contrib/GenomicFeatures_1.8.3.tar.gz'

This seems very strange to me -- it looks like you are running R 2.15
but your installation seems out of date (and biocLite isn't helping
here, even it is an loder version) -- seems like your setup is wonky.

R 2.15 should be using version 2.11 of the bioc "release train". You
need to update lots of things, and you can start with BiocInstaller
(http://bioconductor.org/packages/2.11/bioc/html/GenomicRanges.html),
but perhaps it's a good time to upgrade to R-3.0 and get the latest
and greatest everything (by reinstalling all of your packages with
biocLite) since you need to do a lot of housekeeping work now anyway.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech