[Bioc-devel] graph package conflict with GenomicRanges

[Cook, Malcolm]

Excellent news.  Thanks for the sleuthing and fix.

~Malcolm


> -----Original Message-----
> From: Hervé Pagès [mailto:hpages at fhcrc.org]
> Sent: Friday, November 09, 2012 12:10 AM
> To: Cook, Malcolm
> Cc: bioc-devel at r-project.org
> Subject: Re: graph package conflict with GenomicRanges
> 
> Hi Malcolm,
> 
> The graph package was explicitly creating its own union() generic
> instead of importing it from BiocGenerics. This is fixed in versions
> 1.36.1 (release) and 1.37.1 (devel).
> 
> Thanks for reporting this.
> H.
> 
> 
> On 11/08/2012 09:40 AM, Cook, Malcolm wrote:
> > Hi,
> >
> > I find there is some form of namespace conflict between the GenomicRanges package and 'graph'
> >
> > A session showing reproducible issue, and workaround, follows.
> >
> > Thanks for your help and attention.
> >
> > Malcolm Cook
> > Computational Biology - Stowers Institute for Medical Research
> >
> > PS:  The issue appears very similar to the issue I previously reported
> >
> > 	http://grokbase.com/t/r/bioc-devel/116anxn80x/graph-package-conflict-with-
> rtracklayer/11ab01scy8#201110078thy8az6m72fzc0skpj68tw8bm
> >
> > Which error appears now resolved, thanks to coordination between Martin, Michael,  John, ...????
> >
> >
> > SESSION TRANSCRIPT
> > ---------------------------------------------------------------------------------------------------------------------
> >
> > sh-3.2> R
> >
> > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> > Copyright (C) 2012 The R Foundation for Statistical Computing
> > ISBN 3-900051-07-0
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >
> > ...
> >
> >> source("http://bioconductor.org/biocLite.R"); biocLite(character())
> >
> >   Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> > ...
> >
> >> library(GenomicRanges)
> >
> > Loading required package: BiocGenerics
> >
> > Attaching package: 'BiocGenerics'
> >
> > The following object(s) are masked from 'package:stats':
> >
> >      xtabs
> >
> > The following object(s) are masked from 'package:base':
> >
> >      Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, colnames, duplicated, eval, get, intersect, lapply, mapply, mget, order,
> paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, rownames, sapply, setdiff, table, tapply, union, unique
> >
> > Loading required package: IRanges
> > Warning message:
> > package 'GenomicRanges' was built under R version 2.15.2
> >>   x <- GRanges("chr1", IRanges(c(2, 9) , c(7, 19)), strand=c("+", "-"))
> >    y <- GRanges("chr1", IRanges(5, 10), strand="-")
> >
> >    union(x, y)
> >>>> GRanges with 2 ranges and 0 metadata columns:
> >        seqnames    ranges strand
> >           <Rle> <IRanges>  <Rle>
> >    [1]     chr1   [2,  7]      +
> >    [2]     chr1   [5, 19]      -
> >    ---
> >    seqlengths:
> >     chr1
> >       NA
> >> library(graph)
> >> union(x, y)
> >   Error in as.vector(x) : no method for coercing this S4 class to a vector
> >> GenomicRanges::union(x, y) # workaround - prefix with package
> > GRanges with 2 ranges and 0 metadata columns:
> >        seqnames    ranges strand
> >           <Rle> <IRanges>  <Rle>
> >    [1]     chr1   [2,  7]      +
> >    [2]     chr1   [5, 19]      -
> >    ---
> >    seqlengths:
> >     chr1
> >       NA
> >> sessionInfo()
> > R version 2.15.1 (2012-06-22)
> > 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] graph_1.36.0         GenomicRanges_1.10.4 IRanges_1.16.4       BiocGenerics_0.4.0   BiocInstaller_1.8.3
> >
> > loaded via a namespace (and not attached):
> > [1] parallel_2.15.1 stats4_2.15.1   tools_2.15.1
> >>
> >
> >
> 
> --
> 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
> 
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