[Bioc-sig-seq] generic for strand in genomeIntervals and GenomicRanges

[Julien Gagneur]

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?

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