[Bioc-devel] Some granges() accessors broken in devel

[Peter Hickey]

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