Hej Valerie! Yes, it did fix the issue, but only after I also installed the snow package. Could it be that that's another dependency that has been overlooked in BiocParallel?
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 --------------------------------------------------------------- > On 16 Mar 2015, at 16:09, Valerie Obenchain <voben...@fredhutch.org> wrote: > > 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 >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, Seattle, WA 98109 > > Email: voben...@fredhutch.org > Phone: (206) 667-3158 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
