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WMBEdmands / compMS2Miner

metabolite identification R-package for metabolomic high-resolution LC-MS datasets.
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Error in running example data #7

Open ianchlee opened 4 years ago

ianchlee commented 4 years ago

I am following the example workflow on http://htmlpreview.github.io/?https://raw.githubusercontent.com/WMBEdmands/compMS2Miner/master/vignettes/compMS2Miner_Workflow.html

When I run the following code, it gives an error stating Error in { : task 2 failed - "missing value where TRUE/FALSE needed"

compMS2Demo <- compMS2Construct(MS1features = peakTable, msDataDir = mzXmlDir_example, nCores=nCores, mode = "pos", precursorPpm = 10, ret = 20, TICfilter = 10000)

I am running compMS2 on R-4.0.0.

Thanks, Ian

ianchlee commented 4 years ago

Hi, I tried to run compMS2Construct() by itself to prompt the GUI selection, and the following message is obtained:

creating compMS2 object in positive ionisation mode Select your .mzXML/.mzML/.mgf data directory 2 MS2 (.mzXML) file(s) were detected within the directory... Select your MS1 feature (.csv) file Reading MS1 feature table... ...Done Reading DDA_ACN_80.mzXML... ...DONE extracting metaData from MS2 file ...DONE Of a total of 927 MS2 spectra... 913 MS2 spectra were above the TIC filter of 10000 matching MS1 peak table to precursors of MS2 spectra... Error in if (all(precursorScans == 0)) { : missing value where TRUE/FALSE needed