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:
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
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 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):
 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
 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.