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

[Peter Hickey]

I've no idea what exactly I did or how I did it, but I'd somehow ended
up with some core packages out of sync. Fixed with
BiocInstaller::biocValid() and following advice therein. Sorry for the
noise.

On 20 June 2016 at 21:26, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> 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 you can see that it's outdated.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
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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