[R] multicore/mcparallel error

[Wyatt McMahon]

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.weylandt at gmail.com]
Sent: Tuesday, April 10, 2012 12:07 PM
To: Wyatt McMahon
Cc: R-help at 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 <wmcmahon at 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]]
>
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