[Bioc-devel] ShortRead srdistance is broken

[Nicolas Delhomme]

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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