[BioC] Problem installing GenomicFeatures

[Martin Morgan]

On 03/08/2012 10:01 AM, Georg Otto wrote:
> 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 will likely point to the out-of-date packages with an option to update...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’

I'm guess, but believe it continues to be a stale package version -- 
IRanges, Biostrings, GenomicRanges. From your earlier message

> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.6.7 Biostrings_2.22.0   IRanges_1.13.26
> [4] BiocGenerics_0.1.7
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.8.1   BSgenome_1.20.0 DBI_0.2-5       RCurl_1.91-1
> [5] RSQLite_0.11.1  XML_3.9-4

Bioconductor packages should have even version numbers when in release, 
so your IRanges (and BiocGenerics) seems to be funky (the version for 
R-2-14 is 1.12.6) so I'd try biocLite("IRanges"). Martin
>
> Georg
>
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