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
