Michael, Thanks for your help!
I may not be understanding you. I've upgraded to 2.15. From your text below, I thought the parallel package was included with R 2.15, but I cannot find an mclapply function there. One exists through the multicore package, which I've now installed. I also went looking for a "parallel" package, but was unable to find one. Is there an mclapply included in 2.15? Is there a parallel package I'm missing? Or am I completely misunderstanding your response? Thanks! Wyatt -----Original Message----- From: R. Michael Weylandt [mailto:michael.weyla...@gmail.com] Sent: Tuesday, April 10, 2012 12:07 PM To: Wyatt McMahon Cc: R-help@r-project.org Subject: Re: [R] multicore/mcparallel error I don't know the multicore package, but if possible, it might be easier to upgrade to 2.15 and use the new built-in parallel package that was introduced in R 2.14. Then your syntax would be something like mclapply(files, illumqc) Michael On Tue, Apr 10, 2012 at 11:33 AM, Wyatt McMahon <wmcma...@vbi.vt.edu> wrote: > Hello everyone, > > > > I'm trying to parallelize an R script I have written. To do this, I > am first trying to use the multicore package, because I've had some > previous success with that. > > > > The function I'm trying to parallelize is illumqc. I'd like to create > a separate process for each of 8 files, contained in the vector "files". > > > > Below is my code: > > > > for(i in 1:length(files)){ > > mcparallel(illumqc(files[i]))} > > > > I get the following error: > > > > Error in sendMaster(serialize(try(eval(expr, env), silent = TRUE), > NULL, > : > > ignoring SIGPIPE signal > > Calls: mcparallel -> sendMaster -> .Call > > In addition: Warning message: > > In min(which(alf != 0)) : no non-missing arguments to min; returning > Inf > > > > > > However, if I try and make a simpler example, everything works > correctly, so I'm not sure what's going wrong with this function. Do > I need to post the contents of the function as well? I'm hoping > someone can recognize this error and give me a clue as to what is > going wrong since the function is fairly long. > > > > > > Thanks in advance, > > > > Wyatt > > > > > > > > > > > >> sessionInfo() > > R version 2.13.1 (2011-07-08) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 > > [4] Biostrings_2.20.4 GenomicRanges_1.4.8 IRanges_1.10.6 > > [7] multicore_0.1-7 > > > > loaded via a namespace (and not attached): > > [1] Biobase_2.12.2 grid_2.13.1 hwriter_1.3 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
