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

[Hervé Pagès]

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
>
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>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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