XCMS issue on Linux cluster March 30, 2012, 10:36:17 AM I am trying for the first time to run XCMS on a cluster running linux: > sessionInfo()R version 2.12.2 (2011-02-25)Platform: x86_64-unknown-linux-gnu (64-bit)locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=C LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: stats graphics grDevices utils datasets methods base other attached packages: xcms_1.26.1loaded via a namespace (and not attached): tools_2.12.2When I try to run XCMS on a cdf format Waters Q-TOF data file I get an error message which I haven't seen before.> xset <- xcmsSet(filenames, method = "matchedFilter", fwhm = 8, max = 500, snthresh = 3, step = 0.05, steps = 2, mzdiff = 0.05, index = FALSE, sleep = 0)111101_TwinGene_0095b01: Error in if (del == 0 && to == 0) return(to) : missing value where TRUE/FALSE neededI have run the same data file using the same script on my windows 7 desktop in the past. > sessionInfo()R version 2.13.1 (2011-07-08)Platform: x86_64-pc-mingw32/x64 (64-bit)locale: LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: stats graphics grDevices utils datasets methods base other attached packages: xcms_1.30.3 >I have tried to run mzXML formatted data through both, and that format works well on both the Linux and Windows systems. Obviously, there are differences in both the R version and the XCMS package versions. The problem is that I do not have control of the the Linux cluster, so I was hoping to get some guidance on a potential resolution before requesting R and package upgrades. I have had problems with cdf files previously using centWave, but not matchedFilter - but on the Linux system, I get an error message using either method. Also worth noting - I am not using any of the parallel functions for this - just a single file/core. So I assume it is more likely a Unix/Installation issue rather than a parallel/cluster issue. Any advice is appreciated.