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
