[BioC] 'namespace:Biostrings' error when installing VariantAnnotation

[Steve Lianoglou]

Hi Thomas,

Please use "reply all" when replying to emails on the bioconductor lists so that more people can help you and also so that the back and forths can remain useful to others in general.

That having been said:

On Jun 25, 2013, at 6:45 AM, Thomas Damm Als <tda at hum-gen.au.dk> wrote:

> Hi Steve,
> 
> I have tried installing the package in two ways:
> 
> source("http://bioconductor.org/biocLite.R")
> biocLite("VariantAnnotation")
> 
> library(BiocInstaller)
> biocLite("VariantAnnotation")
> 
> 
> Here's the output from the commands you asked me to run:
>> packageVersion("IRanges")
> [1] Œ1.16.6¹
>> packageVersion("Biostrings")
> [1] Œ2.26.3¹
>> packageVersion("GenomicRanges")
> [1] Œ1.10.7¹

It looks like your version numbers are matching up with the version of R/Bioconductor that you are using, so I'm not sure what's going on.

I'd recommend that you update to the latest version of R (3.0.1) and reinstall your packages via biocLite (I just installed VariantAnnotation without a problem on R-3.0.1), but that advice isn't too helpful if for some reason you need R 2.15.x

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech