Greetings,

I have been using XCMS in R for chemometric analysis for the past few months. Just the last few days the xcmsSet function on my computer (MacPro 10.12.1) (R version 3.3.2 (2016-10-31)) no longer works. Everytime I try to run the peak picking process R stops responding. I have to force quit and restart the program. I have uninstalled R several times, as well as the packages. 

I recently downloaded mzMine2 for Mac OS X and perhaps that has something to do with these issues. Having said that I deleted it and it still does not work. 

I tried the same code (as shown below) on a PC and it had no problems. 

It seems the issue is with my computer, or at least the versions of the packages and R that I have installed. 

Has anyone had this issue before and is there someway I can start using xcms again. 

Other functions such as:

plotChrom(xcmsRaw(junxml[3]),fitgauss=F, rtrange=c(0,1500))

work fine. So something is going on with xcmsSet(). 

Here is the code that no longer works (junxml are my .CDF files, I only have 18 of them)

xset=xcmsSet(junxml, step=0.5, profmethod="bin", fwhm=5, snthresh=2)

Here is my sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xcms_1.50.0         Biobase_2.34.0      ProtGenerics_1.6.0  BiocGenerics_0.20.0 mzR_2.8.0           Rcpp_0.12.8        

loaded via a namespace (and not attached):
 [1] RANN_2.5               lattice_0.20-34        codetools_0.2-15       MASS_7.3-45            MassSpecWavelet_1.40.0 grid_3.3.2             plyr_1.8.4             stats4_3.3.2          
 [9] S4Vectors_0.12.0       Matrix_1.2-7.1         splines_3.3.2          BiocParallel_1.8.1     RColorBrewer_1.1-2     survival_2.39-5        multtest_2.30.0    

Thank you in advance. 

Cheers

I've occasionally seen the combination of a MacBook Pro and BiocParallel in MultiCore mode exhibit this behaviour.  It looks like XCMS makes use of BiocParallel, so if you force it to run process things serially, does it improve?

library(BiocParallel)
register(SerialParam())

xset <- xcmsSet(junxml, step=0.5, profmethod="bin", fwhm=5, snthresh=2)

This is indeed strange. I'm using xcms on a MacBook Pro without any problems. What happens if you call top -o cpu in a terminal - do you see R processes with a %CPU > 0? One side effect of using BiocParallel is that you don't see the progress of the computation, so it might well be that R is calculating.

What happens if you use the CDF files from the faahKO package? Do you get the same problem?

dir(system.file("cdf/KO", package = "faahKO"), full.names = TRUE)