multicore/mcparallel error

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]]

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]]

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]]

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

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

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]]