Hi, Just wanted to let you know I saw this and will get to it as soon as possible.
Valerie On 10/01/2015 05:47 AM, Robert Castelo wrote: > hi Valerie, > > regarding the bug you fixed about a month ago and described below, > there's something still not entirely correct that i did not notice then, > or maybe something has broken since then. Let me run the example again > to explain it: > > library(Biostrings) > library(BiocParallel) > > bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character, > BPPARAM=bpparam("SerialParam")) > [1] "AC" "GT" > > ## this looks fine so far but notice the result when i call > ## now the function 'class()' instead of 'as.character()' > > bpvec(X=DNAStringSet(c("AC", "GT")), FUN=class, > BPPARAM=bpparam("SerialParam")) > [1] "DNAString" "DNAString" > > somehow bpvec() is chopping the input into objects of a class different > to the original input class. this does not happen with the multicore > backend: > > bpvec(X=DNAStringSet(c("AC", "GT")), FUN=class, > BPPARAM=bpparam("MulticoreParam")) > [1] "DNAStringSet" "DNAStringSet" > > > so, i guess there's still something wrong with the SerialParam backend. > > > thanks!! > > robert. > > > On 09/05/2015 12:10 AM, Obenchain, Valerie wrote: >> 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 >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> This email message may contain legally privileged and/or confidential >> information. 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