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Topic: XCMS issue on Linux cluster (Read 1354 times) previous topic - next topic

XCMS issue on Linux cluster

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:
 [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8 
 [7] LC_PAPER=en_US.UTF-8      LC_NAME=C               
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C     

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

other attached packages:
[1] xcms_1.26.1

loaded via a namespace (and not attached):
[1] tools_2.12.2

When 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 needed

I 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:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          LC_TIME=English_United States.1252   

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

other attached packages:
[1] 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.