Skip to content

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

2 messages · Julian Gehring, Hervé Pagès

Original
Julian Gehring
# 
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
2 days later
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: