I was going to say that for the tutorial users it might be easier to
use devtools::install_github('Bioconductor-mirror/GenomicRanges')
rather than svn.However, from https://github.com/Bioconductor-mirror/GenomicRanges/blob/master/DESCRIPTION#L13 you can see that it's outdated. On Mon, Jun 20, 2016 at 6:45 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Pete, > > Because of various issues with the builds, some recent changes to > some core packages have not been able to propagate. So for example > the version of GenomicRanges currently available via biocLite() is > 1.25.4, which is lagging behind the version that is in svn (1.25.8). > I think this could be what is causing the problem you're reporting > (which I cannot reproduce). > > For now the workaround it to install (or re-install) the latest versions > of S4Vectors, IRanges, GenomicRanges, and SummarizedExperiment directly > from svn. > > Sorry for the inconvenience, > > H. > > > On 06/20/2016 11:38 AM, Peter Hickey wrote: >> >> I think this is a recent break. I'm mostly concerned because I need to >> use this "broken" functionality in a tutorial for BioC2016 this week >> and it would require changes to package internals, not the vignette, >> in order to fix this at my end. >> >> library(SummarizedExperiment) >> se <- SummarizedExperiment(rowRanges = GRanges(1, IRanges(1, 10))) >> granges(se) >> # Error in granges(se) : >> # could not find symbol "use.names" in environment of the generic >> function >> # This still works >> rowRanges(se) >> >> Perhaps we should be using rowRanges() rather than granges() but this >> is breaking a few things in minfi and bsseq. I've noticed this on >> granges,RangedSummarizedExperiment-method, but it may affect other >> methods (haven't tested). >> >> Cheers, >> Pete >> >> sessionInfo() >> R version 3.3.0 (2016-05-03) >> Platform: x86_64-apple-darwin13.4.0 (64-bit) >> Running under: OS X 10.11.5 (El Capitan) >> >> locale: >> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 >> >> attached base packages: >> [1] parallel stats4 stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] SummarizedExperiment_1.3.5 Biobase_2.33.0 >> [3] GenomicRanges_1.25.4 GenomeInfoDb_1.9.1 >> [5] IRanges_2.7.6 S4Vectors_0.11.5 >> [7] BiocGenerics_0.19.1 repete_0.0.0.9004 >> [9] devtools_1.11.1 >> >> loaded via a namespace (and not attached): >> [1] Rcpp_0.12.5 codetools_0.2-14 digest_0.6.9 withr_1.0.1 >> [5] plyr_1.8.4 magrittr_1.5 scales_0.4.0 zlibbioc_1.19.0 >> [9] stringi_1.1.1 XVector_0.13.2 pryr_0.1.2 tools_3.3.0 >> [13] stringr_1.0.0 munsell_0.4.3 colorspace_1.2-6 memoise_1.0.0 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- > 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...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
