Excellent news. Thanks for the sleuthing and fix. ~Malcolm
> -----Original Message----- > From: Hervé Pagès [mailto:hpa...@fhcrc.org] > Sent: Friday, November 09, 2012 12:10 AM > To: Cook, Malcolm > Cc: bioc-devel@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 > > E-mail: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
