[Bioc-devel] GRanges construction fails if metadata column is named 'c'

[Hervé Pagès]

Hi Julian,

Thanks for reporting this. The problem should be fixed in GenomicRanges
1.11.31 (this is BioC devel), which will become available via biocLite()
in the next 24 hours or so.

Cheers,
H.

On 02/22/2013 06:19 AM, Julian Gehring wrote:
> Hi,
>
> when constructing a 'GRanges' object with a metadata column named 'c',
> the construction fails with
>
> """
> Error in .getClassFromCache(Class, where) :
>    class should be either a character-string name or a class definition
> """
>
> both in R-2.15.2 and the latest R-devel (2013-02-21 r62017).
>
>
> Here a small example:
> """
> library(GenomicRanges)
>
> ## this works
> gr3 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 4, 3)),
> IRanges(101:110, width=10), b=21:30)
>
> ## let's rename it to 'c', and it fails
> gr3 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 4, 3)),
> IRanges(101:110, width=10), c=21:30)
> """
>
> Best wishes
> Julian
>
> _______________________________________________
> 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