[BioC] Problem installing GenomicFeatures

[Georg Otto]

Martin Morgan <mtmorgan at fhcrc.org> writes:

> On 03/08/2012 08:42 AM, Georg Otto wrote:


>>> install.packages("GenomicFeatures", lib="/home/gwo/rlib")
>> --- Please select a CRAN mirror for use in this session ---
>> Loading Tcl/Tk interface ... done
>> Warning message:
>> In getDependencies(pkgs, dependencies, available, lib) :
>>    package ‘GenomicFeatures’ is not available (for R version 2.14.1)
>
> Maybe you haven't chosen an appropriate Bioconductor repository...
>

i tried several, but to no avail

>>
>>
>> So i tried installation by hand:
>>
>>
>> $ R CMD INSTALL -l ~/rlib GenomicFeatures_1.6.8.tar.gz
>> * installing *source* package ‘GenomicFeatures’ ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Warning: multiple methods tables found for ‘getSeq’
>> Error : classes "file", "connection" are not exported by 'namespace:Biostrings'
>> ERROR: lazy loading failed for package ‘GenomicFeatures’
>>
>>
>> Has anyone an idea what is going on?
>
> It's likely a package version issue, and
>
>   source('http://bioconductor.org/biocLite.R')
>   biocLite(character())
>
> will likely point to the out-of-date packages with an option to update...

in fact, it did update quite a lot of packages, but the instalation of
GenomicFeatures failed:

> biocLite(character())
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Old packages: 'GenomicFeatures', 'leeBamViews', 'rtracklayer'
Update all/some/none? [a/s/n]: a

.
.
.
.

* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
Error : classes "file", "connection" are not exported by 'namespace:Biostrings'
ERROR: lazy loading failed for package ‘GenomicFeatures’

Georg