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.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --------------------------------------------------------------- _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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