[Bioc-devel] graph package conflict with GenomicRanges

[Hervé Pagès]

Hi Malcolm,

On 11/12/2012 08:48 AM, Cook, Malcolm wrote:
> Hi Herve,
>
> Perfect.  I understand the issue, and confirm the fix works for me.

Yes it's related to the discussion we had in the long "parallel package
generics" thread. By doing setGeneric("union") graph was claiming
ownership on this generic, which should be avoided for the reasons
explained in that thread.

Glad the fix works for you and thanks for the confirmation!

Cheers,
H.

>
> Thanks!
>
> Malcolm
>
>
>> 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
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319

-- 
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

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319