Great! Thank you Valerie! robert.
On 9/5/15 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-develThis email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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