Setting the number of CPUs in tune.splsda

Support
1

Hi,
I am trying to tune splsda settings with the following code:
tune.splsda.allsamples ← tune.splsda(gene, phenotype, ncomp = 4, # calculate for first 4 components
validation = ‘Mfold’,
folds = 15, nrepeat = 100, # use repeated cross-validation
dist = ‘centroids.dist’, # use max.dist measure
measure = “BER”, # use balanced error rate of dist measure
test.keepX = list.keepX,
cpus = 10) # allow for paralleliation to decrease runtime

However, I do get an error message…
Error in checkForRemoteErrors(lapply(cl, recvResult)) :
2 nodes produced errors; first error: there is no package called ‘mixOmics’
5.
stop(count, " nodes produced errors; first error: ", firstmsg,
domain = NA)
4.
checkForRemoteErrors(lapply(cl, recvResult))
3.
clusterCall(cl, eval, substitute(expr), env = .GlobalEnv)
2.
clusterEvalQ(cl, library(mixOmics))
1.
tune.splsda(gene, phenotype, ncomp = 4, validation = “Mfold”,
folds = 15, nrepeat = 100, dist = “centroids.dist”, measure = “BER”,
test.keepX = list.keepX, cpus = 2)

I run mixOmics v 6.20.0 on R v 4.2.0, Rstudio v2022.07.1 build 554 on windows

2

Unfortunately the cpus parameter is depreciated - it won’t work. I haven’t had a chance to bring over the newer version of parallelisation (BPPARAM) to this function yet.

If you remove the cpus parameter, it should work

3

OK, thank you for the information!