New user - question about unexplained warnings

March 03, 2012, 04:44:49 PM

Hello,
I am wondering about this set of warnings that I get as I run the annotate wrapper in the CAMERA package. The specific question is where do the warnings come from and are they detrimental in any way?

First the session info:
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

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

other attached packages:
[1] CAMERA_1.10.0 xcms_1.30.3 fastICA_1.1-13

loaded via a namespace (and not attached):
[1] Hmisc_3.9-2 RBGL_1.30.1 cluster_1.14.1 graph_1.32.0 grid_2.14.0 igraph_0.5.4-1 lattice_0.20-0 tools_2.14.0

And the actual code:

xs= xcmsSet('sample.mzdata.mzXML', method= 'centWave')
xsa= annotate(xs)
Start grouping after retention time.
Created 283 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 1219
Start grouping after correlation.

Calculating peak correlations in 283 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100

Calculating graph cross linking in 283 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 1530
xsAnnotate has now 1530 groups, instead of 283

Calculating possible adducts in 1530 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
There were 22 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
2: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
3: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
4: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
5: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
6: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
7: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
8: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
9: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
10: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
11: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
12: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
13: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
14: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
15: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
16: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
17: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
18: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
19: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
20: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
21: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used
22: In if (res == -1) { ... :
the condition has length > 1 and only the first element will be used

Re: New user - question about unexplained warnings

Reply #1 – March 04, 2012, 02:04:51 PM

Hi,

this warnings are generated by the findIsotopes function and can be ignored.
With an update to a more recent version
http://http://bioconductor.org/packages/2.10/bioc/html/CAMERA.html
this warning messages is fixed and should not recur.

Carsten