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
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P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
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