checkCountDepth: mcapply not supported on windows

[jenzopr]

Dear Rhonda,

when running your code on windows, the checkCountDepth function gives an error if not explicitly run with NCores = 1.

checkCountDepth(Data = ExampleData, Conditions = Conditions, PLOT = F, FilterCellProportion = list(c(0.1),c(0.1))) 
Error in mclapply(X = 1:length(Genes), FUN = quickreg, InputData = list(LogData,  : 
  'mc.cores' > 1 is not supported on Windows

This has been described before (see thibautjombart/adegenet#109) and the proposed solution is introducing a platform dependency before using mclapply:

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

For fixing the error above, the code snippet has to introduced in GetSlopes.R, line 24.
Best,
Jens

[jenzopr]

The same issue obviously appears if calling the normalization procedure with

DataNorm <- SCnorm(ExampleData, Conditions = Conditions, OutputName = "ExampleData", NCores = 1)

The traceback shows:

> traceback()
8: stop("'mc.cores' > 1 is not supported on Windows")
7: mclapply(X = 1:length(Genes), FUN = quickreg, InputData = list(LogData, 
       SeqDepth, Genes, Tau), mc.cores = NCores)
6: unlist(mclapply(X = 1:length(Genes), FUN = quickreg, InputData = list(LogData, 
       SeqDepth, Genes, Tau), mc.cores = NCores))
5: GetSlopes(DataList[[x]][GeneFilterList[[x]], ], SeqDepthList[[x]], 
       Tau, NCores)
4: FUN(X[[i]], ...)
3: lapply(1:length(Levels), function(x) GetSlopes(DataList[[x]][GeneFilterList[[x]], 
       ], SeqDepthList[[x]], Tau, NCores))
2: checkCountDepth(Data = Data, NormalizedData = NORMDATA, Conditions = Conditions, 
       OutputName = "SCnorm_NormalizedData_FinalK", PLOT = PLOT, 
       FilterCellProportion = FilterCellProportion, FilterExpression = FilterExpression)
1: SCnorm(ExampleData, Conditions = Conditions, OutputName = "ExampleData", 
       NCores = 1)

This time, the issue is not fixed by setting NCores = 1, because the call to checkCountDepth seems not to pass on the NCores argument from the parent function (SCnorm) properly.

Best,
Jens

[rhondabacher]

Thanks for testing this on Windows and your pull request!

[MarinusVL]

Hi Rhonda,

Still seems to be an issue running SCnorm on windows,

Error in mclapply(X = 1:length(Genes), FUN = quickreg, InputData = list(LogData, :
'mc.cores' > 1 is not supported on Windows

Looks like the GetK function doesn't handle the core number correctly.

best Marinus

[rhondabacher]

Hi Marinus, I apologize for that. I have just added a line of code to correct this, it will set the number of cores to 1. Thanks, Rhonda

…

On Mon, Apr 24, 2017 at 1:44 PM, MarinusVL ***@***.***> wrote: Hi Rhonda, Still seems to be an issue running SCnorm on windows, Error in mclapply(X = 1:length(Genes), FUN = quickreg, InputData = list(LogData, : 'mc.cores' > 1 is not supported on Windows Looks like the GetK function doesn't handle the core number correctly. best Marinus — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGTh7Kaob5Nnlf-axdjaElBehmwlBAKQks5rzO13gaJpZM4K-ueS> .

-- Rhonda Bacher Graduate Student Department of Statistics Biotechnology Center (2130) 425 Henry Mall University of Wisconsin-Madison Email: rbacher@wisc.edu Website: https://rhondabacher.github.io

[MarinusVL]

Thanks, that was quick, Marinus 2017-04-24 12:02 GMT-07:00 Rhonda Bacher <notifications@github.com>:

…

Hi Marinus, I apologize for that. I have just added a line of code to correct this, it will set the number of cores to 1. Thanks, Rhonda On Mon, Apr 24, 2017 at 1:44 PM, MarinusVL ***@***.***> wrote: > Hi Rhonda, > > Still seems to be an issue running SCnorm on windows, > > Error in mclapply(X = 1:length(Genes), FUN = quickreg, InputData = > list(LogData, : > 'mc.cores' > 1 is not supported on Windows > > Looks like the GetK function doesn't handle the core number correctly. > > best Marinus > > — > You are receiving this because you modified the open/close state. > Reply to this email directly, view it on GitHub > <#2 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AGTh7Kaob5Nnlf- axdjaElBehmwlBAKQks5rzO13gaJpZM4K-ueS> > . > -- Rhonda Bacher Graduate Student Department of Statistics Biotechnology Center (2130) 425 Henry Mall University of Wisconsin-Madison Email: ***@***.*** Website: https://rhondabacher.github.io — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYVx4lIFMiaexRNGg6IesDmKkNqomhp8ks5rzPHDgaJpZM4K-ueS> .