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WMBEdmands / compMS2Miner

metabolite identification R-package for metabolomic high-resolution LC-MS datasets.
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"missing value where TRUE/FALSE needed" error #8

Open jchaker opened 3 years ago

jchaker commented 3 years ago

Hello,

I am running compMS2Miner on R-4.0.0. and I ran into the same issue with both the example data (from the vignette) and my own data.

When trying to create the compMS2Demo object / running the following code 

compMS2Demo <- compMS2Construct(MS1features = peakTable, msDataDir = mzmlDir, MS2files=MS2files,
                                nCores = nCores,
                                argsCorrNetwork=list(obsNames=obsNames, corrThresh=0.6,
                                                     corrMethod="spearman",
                                                     delta=0.05, MTC="BH"),
                                mode = "pos", precursorPpm = 10, ret = 60,
                                TICfilter = 10000, minPeaks=1, isoWid=4,
                                verbose=TRUE)

I get the following message

creating compMS2 object in positive ionisation mode
4 MS2 (.mzML) file(s) were detected within the directory...
Starting SNOW cluster with 4 local sockets...
matching MS1 peak table features to the following MS2 files: 
Data1.mzML
Data2.mzML
Data3.mzML
Data4.mzML
1 of 4 complete (Data1.mzML).
2 of 4 complete (Data2.mzML).
3 of 4 complete (Data3.mzML).
4 of 4 complete (Data4.mzML).
Error in { : task 1 failed - "missing value where TRUE/FALSE needed"

A similar issue with task 2 failing has already been reported last May, not sure if anything has come of it. Let me know if I can give any additional useful info to help solve this issue.

Thanks, Jade