[Bioc-devel] Bug in Biostrings::reverse?

[Leandro Roser]

I have been able to make it work now, sorry for the previous email.

Best,
  Leandro.

On Mon, Feb 12, 2018 at 4:52 AM, Leandro Roser <learoser at gmail.com> wrote:

>
> Dear BioC,
>
>
> Using the devel version of Biostrings (2.47.9) i am obtaining an error
> message with the 'reverse' function (below an example):
>
>
> subject <- DNAStringSet(c("ATCATGCCATCATGAT", "ATTTGGAATCAT"))
>
> reverse(subject)
>
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘windows’ for signature ‘"DNAString"’
>
>
> The same occurs in Travis with the devel version. The stable version is
> working without errors.
>
> Could this error be due to a bug in the function?
>
>
> This is my sessionInfo():
>
> > sessionInfo()
> R Under development (unstable) (2018-02-08 r74238)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] BiocInstaller_1.29.4        ShortRead_1.37.1
>  [3] GenomicAlignments_1.15.12   SummarizedExperiment_1.9.14
>  [5] DelayedArray_0.5.18         matrixStats_0.53.1
>  [7] Biobase_2.39.2              Rsamtools_1.31.3
>  [9] GenomicRanges_1.31.19       GenomeInfoDb_1.15.5
> [11] Biostrings_2.47.9           XVector_0.19.8
> [13] IRanges_2.13.25             S4Vectors_0.17.31
> [15] BiocParallel_1.13.1         BiocGenerics_0.25.3
>
> loaded via a namespace (and not attached):
>  [1] zlibbioc_1.25.0        lattice_0.20-35        hwriter_1.3.2
>  [4] tools_3.5.0            grid_3.5.0             latticeExtra_0.6-28
>  [7] Matrix_1.2-12          GenomeInfoDbData_1.1.0 RColorBrewer_1.1-2
> [10] bitops_1.0-6           RCurl_1.95-4.10        compiler_3.5.0
>
>
> Thanks,
>
> Leandro
>
>
> --
>
> Leandro Gabriel Roser
>
> UNSAM - Campus Miguelete IIB - Instituto de Investigaciones Biotecnológicas
>
> Av. 25 de Mayo y Francia CP(1650)
>
> San Martín, Prov. de Buenos Aires, Argentina.
>
> Tel. (5411)4006-1500 Fax: (5411)4006-1559
>



-- 

Leandro Gabriel Roser

UNSAM - Campus Miguelete IIB - Instituto de Investigaciones Biotecnológicas

Av. 25 de Mayo y Francia CP(1650)

San Martín, Prov. de Buenos Aires, Argentina.

Tel. (5411)4006-1500 Fax: (5411)4006-1559

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