On 03/28/2011 05:11 AM, Julien Gagneur wrote:
Hi,
both genomeIntervals and the more recent GenomicRanges define a
generic method 'strand'. There is the same issue for the method
'reduce' between IRanges and 'Intervals' (which is on CRAN, not on
Bioconductor). This leads to conflicts for users that load both
packages. Below sample code (the same happens on R 2.13 devel).
How shall we solve that?
In general, specify the package from which the generic comes from
GenomicRanges::strand
genomeIntervals::strand
It would in general be nice to coordinate generics across packages, but
the prospects for that in this particular case are unclear --
genomeIntervals and GenomicRanges have pretty independent and
more-or-less mutually exclusive dependencies.
Martin
Thanks for your advices,
Julien Gagneur
library(GenomicRanges)
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
library(genomeIntervals)
Loading required package: intervals
Attaching package: 'intervals'
The following object(s) are masked from 'package:IRanges':
reduce
Attaching package: 'genomeIntervals'
The following object(s) are masked from 'package:GenomicRanges':
strand, strand<-
grngs = GRanges(seqnames=c("chr1", "chr2"),
ranges=IRanges(start=1:2, end=2:3), strand=c("+","-"))
strand(grngs)
Error in function (classes, fdef, mtable) : unable to find an
inherited method for function "strand", for signature "GRanges"
reduce(grngs)
Error in function (classes, fdef, mtable) : unable to find an
inherited method for function "reduce", for signature "GRanges"
sessionInfo()
R version 2.12.1 (2010-12-16) Platform:
x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale: [1] C
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] intervals_0.13.1 GenomicRanges_1.2.3
IRanges_1.8.9
loaded via a namespace (and not attached): [1] Biobase_2.10.0
genomeIntervals_1.7.4 tools_2.12.1
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