[Bioc-devel] ShortRead srdistance is broken

[Valerie Obenchain]

Hi Nico,

Can you try again with BiocParallel 1.1.16? Likely related to this post,

https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007114.html


Valerie


On 03/16/2015 07:05 AM, Nicolas Delhomme wrote:
> Hej!
>
> Martin I guess that's for you :-) And I suppose it might only be temporary (due to development in BIocParallel/ShortRead), but I stumbled on the following:
>
> library(ShortRead)
> srdistance(DNAStringSet("AAAAAA"),"AAATAA")
>
> fails with the following error:
>
> Error in bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) :
>   error in evaluating the argument 'BPPARAM' in selecting a method for function 'bplapply': Error in registered()[[bpparamClass]] :
>   attempt to select less than one element
>
> All packages freshly updated from Bioc and R devel a month old:
>
>> sessionInfo()
> R Under development (unstable) (2015-02-11 r67792)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.10.2 (Yosemite)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.25.9         GenomicAlignments_1.3.31 Rsamtools_1.19.44        GenomicRanges_1.19.46
> [5] GenomeInfoDb_1.3.13      Biostrings_2.35.11       XVector_0.7.4            IRanges_2.1.43
> [9] S4Vectors_0.5.22         BiocParallel_1.1.15      BiocGenerics_0.13.6
>
> loaded via a namespace (and not attached):
> [1] lattice_0.20-30     bitops_1.0-6        grid_3.2.0          DBI_0.3.1           RSQLite_1.0.0
> [6] zlibbioc_1.13.2     hwriter_1.3.2       latticeExtra_0.6-26 RColorBrewer_1.1-2  tools_3.2.0
> [11] Biobase_2.27.2
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> The Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
>
> Tel: +46 90 786 5478
> Email: nicolas.delhomme at umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
>
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>


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