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

_______________________________________________ Bioc-sig-sequencing
mailing list Bioc-sig-sequencing@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

_______________________________________________
Bioc-sig-sequencing mailing list
Bioc-sig-sequencing@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing

Reply via email to