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

[Leandro Roser]

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

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