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
>
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