Error of xcmsSet with matchedfilter method November 15, 2016, 01:59:56 AM Dear sir or madam, when i use the xcmsSet with matchedfilter method, the problems were always existed. i am not sure what happened. Could anyone give help? Thanks! I used the window 7 systerm and 8 core CPU .> traceback()4: stop(.error_bplist(res))3: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)2: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)1: xcmsSet(cdffiles, fwhm = 30, snthresh = 3, step = 0.1, steps = 1, profmethod = "binlin")> xset<-xcmsSet(cdffiles,fwhm = 30, snthresh = 3, step = 0.1, steps = 1,profmethod="binlin")Loading required package: xcmsLoading required package: mzRLoading required package: RcppLoading required package: BiocGenericsLoading required package: parallelAttaching package: 'BiocGenerics'The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLBThe following objects are masked from 'package:stats': IQR, mad, xtabsThe following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.minLoading required package: ProtGenericsLoading required package: BiobaseWelcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.95:229 145:464 195:706 245:921 295:1116 345:1275 395:1391 445:1502 495:1606 545:1706 595:1806 95:226 145:461 195:698 245:910 295:1100 345:1253 395:1368 445:1475 495:1579 545:1679 595:1779 Error: BiocParallel errors element index: 3, 4, 5, 6, 7, 8, ... first error: 'from' cannot be NA, NaN or infiniteIn addition: Warning message:stop worker failed: 'clear_cluster' receive data failed: reached elapsed time limit Sincerely yours,Hemi Luan HKBU Hong Kong Quote Selected
Re: Error of xcmsSet with matchedfilter method Reply #1 – November 15, 2016, 02:17:31 AM You'll probably need to supply a reproducible example (data) to get help for this. Quote Selected 1 Likes
Re: Error of xcmsSet with matchedfilter method Reply #2 – November 15, 2016, 03:16:24 AM Quote from: Jan Stanstrup – on November 15, 2016, 02:17:31 AMYou'll probably need to supply a reproducible example (data) to get help for this.Thanks. Jan Quote Selected
Re: Error of xcmsSet with matchedfilter method Reply #3 – November 15, 2016, 03:20:24 AM Quote from: Jan Stanstrup – on November 15, 2016, 02:17:31 AMYou'll probably need to supply a reproducible example (data) to get help for this.I have add a code << snowparam <- SnowParam(workers = 1, type = "SOCK") << set1a <- xcmsSet(cdffiles[1], method = "matchedFilter", fwhm = 3,snthresh = 3, BPPARAM = snowparam)The BPPARAM problems seems to be disappeared. However, the other error was produced. I don't know how to fix it.traceback()13: stop(e)12: value[[3L]](cond)11: tryCatchOne(expr, names, parentenv, handlers[[1L]])10: tryCatchList(expr, classes, parentenv, handlers)9: tryCatch({ FUN(...) }, error = handle_error)8: withCallingHandlers({ tryCatch({ FUN(...) }, error = handle_error) }, warning = handle_warning)7: FUN(X[], ...)6: lapply(X, FUN, ...)5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)3: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)2: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)1: xcmsSet(cdffiles, method = "matchedFilter", fwhm = 3, snthresh = 3, BPPARAM = snowparam)95:423 145:857 195:1267 245:1549 295:1737 345:1849 395:1867 445:1887 495:1905 545:1935 595:1951 95:453 145:909 195:1373 245:1755 295:2043 345:2231 395:2299 445:2339 495:2351 545:2357 595:2357 95:443 145:903 195:1365 245:1733 295:2003 345:2171 395:2233 445:2265 495:2277 545:2277 595:2277 Error in seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * : 'from' cannot be NA, NaN or infiniteIn addition: Warning messages:1: In xcmsRaw(arg$file, profmethod = params$profmethod, profparam = params$profparam, : There are identical scantimes.2: In min(x) : no non-missing arguments to min; returning Inf3: In max(x) : no non-missing arguments to max; returning -Infdo you have any suggestion? ThanksSincerely yours,Hemi Quote Selected
Re: Error of xcmsSet with matchedfilter method Reply #4 – November 15, 2016, 03:26:03 AM I am not sure this can be resolved without one of those files. Seems there is something strange about them."There are identical scantimes." seems to be the hint. That is quite strange how that is possible. Did you run several things at the same time (MS1, data-dependant scans etc)?This seem similar: http://www.metabolomics-forum.com/index.php?topic=530.msg1675#msg1675 What XCMS version are you using? Quote Selected