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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