Open meowcat opened 3 months ago
fileName <- system.file("spectra.Glucolesquerellin/Glucolesquerellin_2184_1.mzML", package="RMassBankData")
setReplicate <- xcms::xcmsSet(files=fileName, method="MS1")
This seems like a very normal XCMS call to me, but something must have changed there.
Hi Michele, thanks for the report! The call does not produce an error here, but simply empty non-data. It is supposed to return Tandem MS or MS$^n$ Mass Spectrometry precursor peaks as annotated in XML raw file,
An "xcmsSet" object with 1 samples
Time range: NA-NA seconds (NA-NA minutes)
Mass range: 0-0 m/z
Peaks: 60 (about 60 per sample)
Peak Groups: 0
Sample classes: spectra.Glucolesquerellin
Feature detection:
o Peak picking performed on MS1.
Profile settings: method = bin
step = 0.1
Memory usage: 0.0154 MB
> peaks(xs)
mz mzmin mzmax rt rtmin rtmax into maxo sn sample
[1,] 0 0 0 NA NA NA 0 0 0 1
[2,] 0 0 0 NA NA NA 0 0 0 1
[3,] 0 0 0 NA NA NA 0 0 0 1
....
And seems the issue is in also mzR, which is not providing precursor mass etc:
library(mzR)
fileName <- system.file("spectra.Glucolesquerellin/Glucolesquerellin_2184_1.mzML", package="RMassBankData")
ms <- openMSfile(fileName)
> head(header(ms)[,c("acquisitionNum", "msLevel", "peaksCount", "retentionTime", "precursorScanNum", "precursorMZ")])
acquisitionNum msLevel peaksCount retentionTime precursorScanNum precursorMZ
1 337 2 55 226.0152 NA 0
2 338 2 57 226.6848 NA 0
3 339 2 50 227.3550 NA 0
Yours, Steffen
The build works now, though the underlying issue is unresolved (and on 3.20 Win it still fails but this is a network issue)
I guess this will resolve itself but I have to check