[Bioc-devel] graph package conflict with GenomicRanges

[Hervé Pagès]

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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