Obscure error with findPeaks.matchedFilter January 08, 2015, 08:24:54 AM Dear all,I'm using the latest xcms with R 3.0.2 on x86_64-suse-linux-gnu (64-bit).I've encountered a problem with findPeaks.matchedFilter which I can't find anything about in this forum or indeed anywhere.Funny thing is, the same code runs smoothly on Windows 7 / 64bit with R 2.15.3.This is the error:Fehler in doubleMatrix(num, length(zidx)) : das dims Argument enthält fehlende Werte(sorry for the German. It translates to: "Error in doubleMatrix(num, length(zidx)): the dims argument contains missing values")traceback()14: .Call("DoubleMatrix", as.integer(nrow), as.integer(ncol), PACKAGE = "xcms")13: doubleMatrix(num, length(zidx))12: profFun(object@env$mz, object@env$intensity, object@scanindex, num, minmass, maxmass, FALSE, object@profparam)11: `profStep<-`(`*tmp*`, value = 0.5)10: `profStep<-`(`*tmp*`, value = 0.5)9: split.xcmsRaw(object, f = keepidx)8: split(object, f = keepidx)7: .local(object, ...)6: findPeaks.matchedFilter(xraw, fwhm = fuwihama, sigma = fuwihama/2.3548, max = maxpeaks, snthresh = snlevel, step = stepsize, steps = nofsteps, mzdiff = mzdifference)5: findPeaks.matchedFilter(xraw, fwhm = fuwihama, sigma = fuwihama/2.3548, max = maxpeaks, snthresh = snlevel, step = stepsize, steps = nofsteps, mzdiff = mzdifference) at tmptDMo6q.R#4044: eval(expr, envir, enclos)3: eval(ei, envir)2: withVisible(eval(ei, envir))1: source("tmptDMo6q.R")The mass spectrum (from LC/MS) is a cdf converted from ChemStation and loads fine:> xrawAn "xcmsRaw" object with 314 mass spectraTime range: 5.4-361.2 seconds (0.1-6 minutes)Mass range: 321.1-1931.9 m/zIntensity range: 150-75984MSn data on 0 mass(es) with 0 MSn spectraProfile method: binlinProfile step: 0.5 m/z (3223 grid points from 321 to 1932 m/z)Memory usage: 7.96 MBThe mass spectrum was recorded with a pretty high threshold so it looks kind of sparse. Some scans do not contain any data points at all.This is the output of xraw@scanindex: [1] 0 0 0 0 1 3 5 7 10 12 14 18 [13] 23 27 33 39 43 45 46 49 53 58 62 65 [25] 67 67 68 69 70 71 71 71 71 71 71 71 [37] 71 71 71 71 71 71 71 73 75 77 78 79 [49] 80 80 81 81 81 81 81 81 81 84 89 96 [61] 101 108 113 117 122 128 134 142 152 164 177 199 [73] 232 278 340 413 481 537 586 633 681 729 779 836......My suspicion is that is has something to do with that. Just strange that Windows seems to ignore that.Anyone any ideas how to patch this? I need the linux version since it runs on our webserver that processes mass spectra and outputs data via CGI's.Any help highly appreciated. I hope I didn't leave anything out.Thanks in advance,Tobias Quote Selected