'mc.cores' > 1 is not supported on Windows

[knausb]

Hello,

I have a function 'vcfR2genelight' which I'm using to convert an object from a package I'm working on called vcfR to genlight objects. This function calls adegenet::as.genlight on a matrix of genotypes to create the genlight object. On Windows this currently throws an error:

>     x <- adegenet::as.genlight(t(x))
Error in mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i,  : 
  'mc.cores' > 1 is not supported on Windows

This appears to be because Windows does not support forking. In trying to find a solution I found:

http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2013-July/000681.html

But that did not appear to resolve the issue. I've also made an attempt with:

x <- adegenet::as.genlight(t(x), n.cores=1)

With the hope I could pass that information on. But it generated the same error. I feel there should be a way for Windows users to set mc.cores to 1 but can't figure it out. Any suggestions? Or is there something I've overlooked?

If you want to handle this within adegenet perhaps something like:

if( .Platform$OS.type == "windows" ){
  n.cores = 1
}

might provide a solution?

Thank you for any help!
Brian

[thibautjombart]

Hi there,
I like the suggestion. Fork & pull request? ;)
Cheers
Thibaut

On Wed, Nov 18, 2015 at 2:13 PM, Brian Knaus notifications@github.com
wrote:

Hello,

I have a function 'vcfR2genelight' which I'm using to convert an object
from a package I'm working on called vcfR to genlight objects. This
function calls adegenet::as.genlight on a matrix of genotypes to create the
genlight object. On Windows this currently throws an error:

x <- adegenet::as.genlight(t(x))

Error in mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i, :
'mc.cores' > 1 is not supported on Windows

This appears to be because Windows does not support forking. In trying to
find a solution I found:

http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2013-July/000681.html

But that did not appear to resolve the issue. I've also made an attempt
with:

x <- adegenet::as.genlight(t(x), n.cores=1)

With the hope I could pass that information on. But it generated the same
error. I feel there should be a way for Windows users to set mc.cores to 1
but can't figure it out. Any suggestions? Or is there something I've
overlooked?

If you want to handle this within adegenet perhaps something like:

if( .Platform$OS.type == "windows" ){
n.cores = 1
}

might provide a solution?

Thank you for any help!
Brian

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Reply to this email directly or view it on GitHub
#109.

[thibautjombart]

Fixed at ad56026