Hi Robert,
Thanks for reporting the bug. The problem was with how 'X' was split
before dispatching to bplapply() and affected both SerialParam and
SnowParam. Now fixed in release (1.2.21) and devel (1.3.52).
Valerie
>
> ----- Forwarded Message -----
> From: "Robert Castelo" <robert.cast...@upf.edu>
> To: bioc-devel@r-project.org
> Sent: Wednesday, September 2, 2015 8:12:33 AM
> Subject: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem
>
> hi,
>
> I have encountered a problem when using the bpvec() function from the
> BiocParallel package with DNAStringSet objects and the "SerialParam"
> backend:
>
> library(Biostrings)
> library(BiocParallel)
>
>
> ## all correct when using the multicore backend
>
> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character, BPPARAM=bpparam())
> [1] "AC" "GT"
>
> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character,
> BPPARAM=MulticoreParam())
> [1] "AC" "GT"
>
>
> ## problem when using the SerialParam backend
>
> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character,
> BPPARAM=bpparam("SerialParam"))
> [1] "1" "2"
>
>
> the problem is that elements of the DNAStringSet object get somehow
> coerced to integers when using the "SerialParam" backend.
>
>
> this occurs in both current release and devel, please find the
> corresponding sessionInfo()'s below.
>
>
> thanks!
>
> robert.
>
> ## release
> sessionInfo()
> R version 3.2.0 (2015-04-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> Running under: Fedora release 12 (Constantine)
>
> locale:
> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
> [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
> [7] LC_PAPER=en_US.UTF8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4 parallel stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] BiocParallel_1.2.20 Biostrings_2.36.4 XVector_0.8.0
> [4] IRanges_2.2.7 S4Vectors_0.6.5 BiocGenerics_0.14.0
> [7] vimcom_1.2-3 setwidth_1.0-4 colorout_1.1-0
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.14.0 futile.logger_1.4.1 tools_3.2.0
> [4] lambda.r_1.1.7 futile.options_1.0.0
>
> ## devel
> sessionInfo()
> R Under development (unstable) (2015-04-28 r68268)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> Running under: Fedora release 12 (Constantine)
>
> locale:
> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
> LC_TIME=en_US.UTF8
> [4] LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
> LC_MESSAGES=en_US.UTF8
> [7] LC_PAPER=en_US.UTF8 LC_NAME=C LC_ADDRESS=C
>
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4 parallel stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] BiocParallel_1.3.51 Biostrings_2.37.8 XVector_0.9.3
> IRanges_2.3.18
> [5] S4Vectors_0.7.14 BiocGenerics_0.15.6 vimcom_1.0-0
> setwidth_1.0-4
> [9] colorout_1.0-3
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.15.0 futile.logger_1.4.1 tools_3.3.0
> lambda.r_1.1.7
> [5] futile.options_1.0.0
>
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