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Problems with the fillpeak step

Hi,

I have some error messages with the fillpeak step that I don't know how to solve "Error in seq.default (floor(mrange[1]step) * step, ceiling(mrange[2]step) * : ‘from’ cannot be NA, NaN  or infinite" (cf file attached).
Versions of R and xcms are recent (reinstalled yesterday). I attached as well the script that I am currently using (it was working on other MS data acquired on the equipment the same day).

Can you help me?
Many thanks in advance for your answer.
Regards.

[attachment deleted by admin]

Re: Problems with the fillpeak step

Reply #1
Did you find out what was causing this issue? I am having the same problem.

Re: Problems with the fillpeak step

Reply #2
I also just ran into this problem.  I'm not sure what the cause is.  For me the error message happened during a call to `getEIC()`

Re: Problems with the fillpeak step

Reply #3
Also having this problem in the density step:  'error in density.default(speakmat[,"rt"], bw, from='retrange[1]-3*: 
non-finite 'from'

I reverted to an xcms installation from a previous R version and the problem went away on the same dataset, so I think it has to do with a new XCMS version.  I can't say for certain it isn't also dependent on a new R version at this point.  

Functional:
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xcms_1.40.0         Biobase_2.24.0      BiocGenerics_0.10.0 mzR_1.10.7          Rcpp_0.12.1        

loaded via a namespace (and not attached):
[1] codetools_0.2-8 tools_3.1.1 


NONFUNCTIONAL: 
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xcms_1.48.0         Biobase_2.32.0      ProtGenerics_1.4.0  BiocGenerics_0.18.0 mzR_2.6.2           Rcpp_0.12.5        

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 codetools_0.2-14   grid_3.3.1         lattice_0.20-33  

 

Re: Problems with the fillpeak step

Reply #4
Just tested new R (3.3.1) and older XCMS (1.46.0) and the error is gone.  I will be using this version until a newer is released. 
Corey