Uploading error message?

October 14, 2011, 11:36:26 AM

Hi I was wondering if anyone has come across this error before when uploading your cdf files. The upload commences and completes 50 or so files but always seems to halt on this particular file? I'm puzzled. Thanks for your help.

ASP_P_P2_5901:
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">)
5: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
6: do.call(method, list(object, ...))
7: .local(object, ...)
8: findPeaks(lcraw, ...)
9: findPeaks(lcraw, ...)
10: xcmsSet()
Error in profFun(object@env$mz, object@env$intensity, object@scanindex, :
caught access violation - continue with care
In addition: Warning message:
In xcmsRaw(files, profmethod = profmethod, profparam = profparam, :
There are identical scantimes.

Re: Uploading error message?

Reply #1 – October 15, 2011, 11:07:36 AM

I'm a little confused by the term "uploading" since you aren't uploading anything, but processing your files with XCMS locally.

Quote

In xcmsRaw(files, profmethod = profmethod, profparam = profparam, :
There are identical scantimes.

It seems like this is the problem: some data files seem to be corrupted, there shouldn't be scans with identical scantimes.
The profiling method crashes when it tries to create the profile matrix from the raw data.

Re: Uploading error message?

Reply #2 – October 18, 2011, 01:47:08 AM

Thank you Ralf,

Apologies I am just familiarising with XCMS "uploading" is purely a misunderstanding, the error messages can be rather cryptic for the uninitiated but there is a wealth of information available.