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

[Martin Morgan]

On 06/20/2016 09:22 PM, Leonardo Collado Torres wrote:
> I was going to say that for the tutorial users it might be easier to
> use devtools::install_github('Bioconductor-mirror/GenomicRanges')

FWIW biocLite("Bioconductor-mirror/GenomicRanges") invokes 
install_github(). Martin

> 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 you can see that it's outdated.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
>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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