I changed my computer and re-installed the whole packages, with the latest R version (3.5.1). Since then, xcms does not work anymore, remaining stacked at the first line
xset<-xcmsSet(method="centWave", peakwidth=c(3,20), snthresh=5, mzdiff=0.01, ppm=3, prefilter=c(5,100000), noise=20000, integrate=1)
xset
a warning message indicate :
Scanning files in directory C:/users/.... (blablabla until the correct file directory).. found 99 files
I also tried with the old R version that I installed and that used to work, but no success either
I'm not a beginner with xcms, and I tried to process my files using another computer in the lab and everything is alright.
I'm using windows 10 with an dell computer equipped with a Xeon processor
any idea of what'sgoing wrong?
many thanks
jc
Eventually there is something strange going on with the parallel processing. Please add the following line right after you load the xcms package and retry:
library(xcms)
register(SerialParam())
with that you disable parallel processing - if it runs without parallel processing we can think of a way to fix parallel processing.
cheers, jo