Error in object@backend$getAllScanHeaderInfo()

[ghost]

Hi,

I've just started IPO recently to analyze non targeted LC/qTOF/MS data (mzXML files). Unfortunately, I got issue at the first step. The script is as below:

data<-list.files(, recursive=T,full.names=T)

library(IPO)
library(xcms)

peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave')
peakpickingParameters$ppm <- c(2,15)
peakpickingParameters$min_peakwidth<-c(2,15)
peakpickingParameters$max_peakwidth<- c(10,25)

time.xcmsSet <- system.time({ # measuring time
  resultPeakpicking <- 
    optimizeXcmsSet(files = data[1:10], 
                    params = peakpickingParameters, 
                    nSlaves = 1, 
                    subdir = NULL,
                    plot = TRUE)
})

And I got the error like:

Error in xcms::xcmsSet(files = files, method = "centWave", peakwidth = c(xcmsSetParameters$min_peakwidth[task],  : 
  Chromatographic peak detection failed for all files! The first error was: Error in object@backend$getAllScanHeaderInfo(): upper value must be greater than lower value
Timing stopped at: 0.01 0.01 8.7

And then I skipped the IPO part and just try XCMS right away.

xset <- xcmsSet(data, method="centWave",  ppm = 10, peakwidth = c(2, 24), snthresh = 5,
                prefilter = c(3, 100))

But I got same error again. I really couldn't find the solution yet. It is working with faahKO tutorials and I updated all packages and R but still didn't work. I would appreciate if you help me. Thanks in advance for your time.

[rietho]

Thanks for using IPO 😄

As the same error occurs on using xcmsSet, this seems to be an issue with the xcms-package. Please report it there and link back to this issue for keeping track.