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

[Martin Morgan]

On 06/25/2013 04:47 PM, Steve Lianoglou wrote:
> 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 think Steve is on the right track; it could be GenomicFeatures, or you might 
discover the problem with

   trace(loadNamespace, quote(print(package)))
   library(GenomicFeatures)

you'll a package name printed each time a dependency is asked to be loaded. 
Probably the last package displayed is the one that is out of sync with your 
installation; compare it with the version available at

   http://bioconductor.org/packages/2.11/bioc/html/GenomicRanges.html

with 'GenomicRanges' replaced by whatever package appears to be the problem.

For what it's worth (not relevant in this immediate case), in 3.0.1 it might 
have been possible to ask

   BiocInstaller::biocValid()

for some hints.

Martin

> 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
>
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