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

Leonardo Collado Torres lcollado at jhu.edu
Tue Jun 21 03:22:45 CEST 2016


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you can see that it's outdated.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 <hpages at 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 at 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: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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