[Bioc-devel] GenomicFeatures on 2.13.1 Windows

Hervé Pagès hpages at fhcrc.org
Tue Aug 2 03:01:51 CEST 2011


Hi Dario,

Seems like you are trying to use the devel version of GenomicFeatures
with BioC release. Not a good idea...

Cheers,
H.


On 11-07-28 08:00 PM, Dario Strbenac wrote:
> Hello,
>
> I'm having some troubles loading GenomicFeatures. I'm on a Windows 7 64 bit PC. This is the output I see, in a new session of R.
>
>> library(GenomicFeatures)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>      cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
> Loading required package: GenomicRanges
> Error : class "Sequence" is not exported by 'namespace:IRanges'
> Error: package/namespace load failed for 'GenomicFeatures'
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.4.6 IRanges_1.10.4
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.6.0     Biostrings_2.20.1 BSgenome_1.20.0   DBI_0.2-5         RCurl_1.5-0.1     RSQLite_0.9-4     XML_3.2-0.2
>> GRanges()
> GRanges with 0 ranges and 0 elementMetadata values
>       seqnames ranges strand |
>
> seqlengths
>
>
>> IRanges()
> IRanges of length 0
>
> Strangely, GenomicRanges seems to have been loaded, although the loading gave an error message.
>
> In another new R session, I can load GenomicRanges just fine.
>
>> library(GenomicRanges)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>      cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
>      pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.4.6 IRanges_1.10.4
>
> Does anyone else have the same problem ?
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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