Error in gapfiller

Skip to first unread message

Oct 29, 2015, 8:00:45 AM10/29/15
to Ideom

I'm currently encountering a error in the PeakML.GapFiller function " Error in ls(envir = envir, all.names = private):invalid 'envir' argument . I'm running the Script (XCMS mzmatch pipeline) on a Linux server and this error occurs especially with large data sets. Could anybody please provide some help to avoid this error?



Andris Jankevics

Oct 29, 2015, 8:50:37 AM10/29/15
to, Ideom
Hi Daniel, 

I will need more details to be able to help you. This R error message is generic and can be related to many issues.
Can you send full R console output and command with parameters you used for a GapFiller function?

Best Regards,

Geschäftsführer: Dr. Nicolas Schauer
Handelsregister: Amtsgericht Potsdam
HRB: 22137P, USt-IdNr. DE 26614398

You received this message because you are subscribed to the Google Groups "Ideom" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
Visit this group at
For more options, visit

Oct 29, 2015, 10:10:55 AM10/29/15
to Ideom
Hello Andris,

thanks for the fast reply. The gap filler options are: PeakML.GapFiller(nSlaves=cores,
  filename = "combined_highintensity.peakml", ionisation = "detect", Rawpath = source.path, 
  outputfile = "highintensity_gapfilled.peakml", ppm=10, rtwin = 0

The console runs through my mzxml files ((Extracting peak data from PeakMl file,Peak data created in 692.179 s) and aborts with the given error message. The error occurs at the very end of the list of mzxml files. I hope this is a little bit more helpful.


Reply all
Reply to author
0 new messages