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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">I have recently updated to R-3.0.1 and to adegenet 1.3-9 the adegenet scripts I was running successfully in R-3.0.0 adgenet 1.3-8 are now failing when calling the new("genlight")
functions, if there are arguments. I would be happy to set mc.cores to 1 but can not seem to pass this argument successfully. Help appreciated. Code is as follows:<br>
<br>
> new("genlight")<br>
=== S4 class genlight ===<br>
0 genotypes, 0 binary SNPs<br>
> x <- new("genlight")<br>
> x<br>
=== S4 class genlight ===<br>
0 genotypes, 0 binary SNPs<br>
### Clearly OK<br>
<br>
> data.SNP[1:5, 1:5]<br>
10015_641 c10016_302 c10017_644 c10126_263 10140_297<br>
001031 0 0 2 2 0<br>
001209 2 0 0 2 2<br>
001298 2 0 2 2 0<br>
001765 2 0 2 2 0<br>
001032 2 0 2 2 0<br>
> gl.ALL <- new("genlight", data.SNP, pop=data.annot[, 8], ploidy=2)<br>
Error in mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i, :
<br>
'mc.cores' > 1 is not supported on Windows<br>
> gl.ALL <- new("genlight", data.SNP, pop=data.annot[, 8], ploidy=2, multicore=FALSE)<br>
Error in mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i, :
<br>
'mc.cores' > 1 is not supported on Windows<br>
> gl.ALL <- new("genlight", data.SNP, pop=data.annot[, 8], ploidy=2, multicore=FALSE, mc.cores=1)<br>
Error in mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i, :
<br>
'mc.cores' > 1 is not supported on Windows<br>
> gl.ALL <- new("genlight", data.SNP, pop=data.annot[, 8], ploidy=2, mc.cores=1)<br>
Error in mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i, :
<br>
'mc.cores' > 1 is not supported on Windows<br>
<br>
## Even on the toy example I get<br>
> dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA))<br>
> x <- new("genlight", dat)<br>
Error in mclapply(input$gen, function(e) new("SNPbin", e), mc.cores = n.cores, :
<br>
'mc.cores' > 1 is not supported on Windows<br>
<br>
<br>
> sessionInfo()<br>
R version 3.0.1 (2013-05-16)<br>
Platform: x86_64-w64-mingw32/x64 (64-bit)<br>
<br>
locale:<br>
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
<br>
<br>
attached base packages:<br>
[1] parallel stats graphics grDevices utils datasets methods base
<br>
<br>
other attached packages:<br>
[1] adegenet_1.3-9 genalg_0.1.1 ade4_1.5-2 <br>
<br>
loaded via a namespace (and not attached):<br>
[1] ape_3.0-9 grid_3.0.1 igraph_0.6.5-2 lattice_0.20-15 MASS_7.3-26 nlme_3.1-109 tools_3.0.1
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