Error in fillpeaks after XCMSnExp conversion

[ghost]

Hello,
I would like to annotate my masses
I have xcms version 3.9.2 and camera version 1.43.2.
I do the different stages of processing xcms
and I converted my XCMSnExp to xcmsSet
when I apply the Fillpeaks function, here is the error message:
Error in rowSums(groupmat[, (match( npeaks, colnames(groupmat)) + 1):ncol(groupmat), :
'x' must be numeric
I take exactly the same steps as the MTBLS2 example

Thanks

Yohann

[stanstrup]

Would be helpful to post your whole script starting from conversion of the object.

[ghost]

I precise i have the same error with the MTBLS2 example

[ghost]

waters (.raw) files that I converted via pw (MS1/MSe)
exemple with 8 files

mzmlpath <- "D:/Tau_Ltm/"
mzmlfiles <- list.files(mzmlpath , recursive = TRUE, full.names = TRUE)
list.files(cdfpath, recursive = TRUE)
files = cdffiles

pd<-data.frame(sample_name = sub(basename(files),pattern = ".mzML", replacement = "", fixed = TRUE), stringsAsFactors = FALSE)
raw_data<-readMSData(files, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk")

mslevel

table(msLevel(raw_data))

MS1

cwp <- CentWaveParam(ppm=25, peakwidth=c(2,25), mzdiff=0.01, snthresh=10 , prefilter=c(3,100),noise = 0)
xdata <- findChromPeaks(raw_data, param = cwp)

MS2

xdata <- findChromPeaks(xdata, param = cwp1, msLevel = 2L, add = TRUE)

grouping

pdp <- PeakDensityParam(sampleGroups = rep(1, length(fileNames(xdata))),minFraction = 0.8)
xdata <- groupChromPeaks(xdata, param = pdp)

###retention time correction
xdata <- adjustRtime(xdata, param = ObiwarpParam(binSize = 0.6))

grouping

xdata <- groupChromPeaks(xdata, param = pdp )
xdata <- groupChromPeaks(xdata, param = pdp , msLevel = 2L, add = TRUE)

fillpeaks

processed_Data <- fillChromPeaks( xdata, param = FillChromPeaksParam(fixedRt = medWidth))
processed_Data <- fillChromPeaks(xdata, param = FillChromPeaksParam(fixedRt = medWidth), msLevel = 2L)

annotation via camera

xset <- as(filterMsLevel(processed_Data, msLevel = 1L), "xcmsSet")
sampclass(xset) <- rep(1, length(fileNames(xdata)))
gdata <- fillPeaks(xset )

and then the error message
Error in rowSums(groupmat[, (match("npeaks", colnames(groupmat)) + 1):ncol(groupmat), :
'x' doit être numérique