ERROR: Caught segfault 'memory not mapped'

March 01, 2012, 05:28:47 PM

Hi all,

I was hoping someone could help me with the following error. I am using XCMS to analyse 80 LCMS runs of four different solvent extractions. Using PCA, I hope to visualise the variability associated with each different extraction technique. LCMS conditions are the same for all 80 runs. Anyway, it takes a couple of hours for XCMS to filter and align my 80 runs but when it gets to the last 20 or so runs (the last 20 runs are the aqueous phase of a MeOH:DCM:H2O extraction and look very different to the other 60 runs) I get the error below. After "googling" the error it seems there may be an issue with the C code. I haven't tried using the faahKO data set as I suspect it wont occur. Can anybody Help?

Cheers,

Ben

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R version (Mac): R for 2.14.1 GUI 1.43 Leopard build 32-bit
XCMS version (Mac): 1.30.3
XQuartz 2.6.3

*** caught segfault ***
address 0xacbd0128, cause 'memory not mapped'

Traceback:
1: .C("ProfBinM", x, y, as.integer(length(x)), as.integer(zidx), as.integer(length(zidx)), as.double(xstart), as.double(xend), as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
2: profFun(object@env$mz, object@env$intensity, object@scanindex, bufsize, mass[1], mass[bufsize], TRUE, object@profparam)
3: .local(object, ...)
4: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">, fwhm = 12, mzdiff = 0.02, step = 0.02)
5: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">, fwhm = 12, mzdiff = 0.02, step = 0.02)
6: do.call(method, list(object, ...))
7: .local(object, ...)
8: findPeaks(lcraw, ...)
9: findPeaks(lcraw, ...)
10: xcmsSet(xfiles, fwhm = 12, mzdiff = 0.02, step = 0.02)
11: eval.with.vis(expr, envir, enclos)
12: eval.with.vis(ei, envir)
13: source("xcms_preprocess_BG.r")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

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Re: ERROR: Caught segfault 'memory not mapped'

Reply #1 – March 01, 2012, 09:32:23 PM

Problem Solved. It appears that one of my netCDF files was corrupt. It pays to check them after exporting!!