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.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
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