Re: runParallel slot in xsAnnotate
Reply #2 –
Thank you Carsten,
While trying to initialize the xsAnnotate objects with multiple cores, I discovered that the "snow" part in the code was missing (CAMERA 1.6.0). There is no problem with this, I added it it myself (the chunk below), but is it supposed to be like this or there is a minor bug there? In addition, are the CAMERA functions parallelized or not yet implemented? I am asking because groupCorr is not really running faster and there isn't any core activity beyond usual. From a fast look at the source they don't seem to be implemented for parallel calculations. Is it so or am I missing something?
The missing part for the initialization with "snow" (taken from the initialization of xcmsSet object):
...
else
{
snow = "snow"
if (try(require(snow, character.only = TRUE, quietly = TRUE)))
{
cat("Starting snow cluster with", nSlaves, "local sockets.n")
snowclust <- makeCluster(nSlaves, type = "SOCK")
runParallel <- 1
parMode <- "SOCK"
}
}
...
Thank you in advance!
Panos