[BioC] Problem installing GenomicFeatures

Georg Otto gwo at well.ox.ac.uk
Fri Mar 9 12:26:00 CET 2012

Martin Morgan <mtmorgan at fhcrc.org> writes:

> 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:

>> 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

I updated IRanges and BiocGenerics, but that did not help
either. Finally, I completely removed my Bioconductor installation and
reinstalled everything. Now it works again and I was able to install
GenomicFeatures. Thanks a lot for your help.


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