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Messages - lhemivw

1
RMassBank / Error??

I used the example file in RMassBankData. The error could not be resolved.

loadList("Compoundlist.csv")
Error in loadList("Compoundlist.csv") : 
  Unable to interpret the SMILES-strings for ID(s) 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2758 
Please check these and load the list again.


Best,
Hemi
2
XCMS / Re: Error of xcmsSet with matchedfilter method
Quote from: Jan Stanstrup – on
You'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 infinite
In 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 Inf
3: In max(x) : no non-missing arguments to max; returning -Inf

do you have any suggestion? Thanks

Sincerely yours,
Hemi
4
XCMS / Error of xcmsSet with matchedfilter method
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: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The 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.min

Loading required package: ProtGenerics
Loading required package: Biobase
Welcome 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 infinite
In addition: Warning message:
stop worker failed:
  'clear_cluster' receive data failed:
  reached elapsed time limit 


Sincerely yours,
Hemi Luan 
HKBU 
Hong Kong
5
XCMS / the error was produced in XCMS
Hi, all
  Could you tell me how to solve this problem?

Thank you

Hemi
<
Loading required package: methods
Loading required package: mzR
Loading required package: Rcpp
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object(s) are masked from 'package:xcms':

    phenoData, phenoData<-

Warning message:
In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

There were 50 or more warnings (use warnings() to see the first 50)
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: diffreport -> diffreport -> .local -> write.table -> file
In addition: Warning messages:
1: In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 6,8,88,133,140,147,148,150,185,192,200,272,277,287,292,377,395,401,409,422,428,430,548,566,604,606,628,716,739,835,873,1026,1097,1424,1464,1548,2057 --> row.names NOT used
2: In file(file, ifelse(append, "a", "w")) :
  cannot open file 'CHD_URINE.tsv': Permission denied
Execution halted>
6
XCMS / QE error xcms
Dear everyone?
        when i use the xcms to process the data (1.8G) obtained from thermo QE, the error was happened. Could anyone give me a help? thank you

    Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object(s) are masked from 'package:xcms':

    phenoData, phenoData<-

1-1: 3: >/ifs1/ST_PRO/USER/chenxiaomin/QEtest/1/1-1.mzXML

 *** caught segfault ***
address 0x1099ced0, cause 'memory not mapped'
Segmentation fault

Best wishes,
Hemi
8
XCMS / centwave-scanrange
Hi,
    I got a problem with the centwave-scanrange. I want to select a range of data using the scantime, however, the centwave only have the scanrange function.

my question is how to get the scanrange. I found that the the scanrange (scan index) is not the scan number.

.@ env                  :<environment: 0x02fb58e0>
  ..@ tic                  : num [1:1377] 30161494 29720700 30073236 29816570 29062580 ...
  ..@ scantime            : num [1:1377] 6.07 6.94 7.8 8.69 9.55 ...
  ..@ scanindex            : int [1:1377] 0 1006 2005 2995 4035 5069 6038 7052 8087 9132 ...
  ..@ polarity            : Factor w/ 3 levels "negative","positive",..: 2 2 2 2 2 2 2 2 2 2 ...
  ..@ acquisitionNum      : int [1:1377] 1 7 13 19 25 31 37 43 49 55 ...
  ..@ profmethod          : chr "bin"
  ..@ profparam            : list()
  ..@ mzrange              : num [1:2] 50 1500
  ..@ gradient            : logi[0 , 0 ]
  ..@ msnScanindex        : int(0)
  ..@ msnAcquisitionNum    : int(0)
  ..@ msnPrecursorScan    : int(0)
  ..@ msnLevel            : int(0)
  ..@ msnRt                : num(0)
  ..@ msnPrecursorMz      : num(0)
  ..@ msnPrecursorIntensity: num(0)
  ..@ msnPrecursorCharge  : num(0)
  ..@ msnCollisionEnergy  : num(0)
  ..@ filepath            : chr "QC8.mzXML"