[Bioc-devel] ShortRead srdistance is broken

[Nicolas Delhomme]

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.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

> On 16 Mar 2015, at 16:09, Valerie Obenchain <vobencha at 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.delhomme at umu.se
>> SLU - Umeå universitet
>> Umeå S-901 87 Sweden
>> ---------------------------------------------------------------
>> 
>> _______________________________________________
>> Bioc-devel at 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: vobencha at fredhutch.org
> Phone: (206) 667-3158