Steffen Neumann

But, partly successful. I don't think it is the missing instrument that breaks xcms: ``` library(xcms) ms length(peaks(ms)) [1] 2801 > peaks(ms)[c(1, 666, 2801)] [[1]] mz intensity [1,] 241.4680 5891.645...

One more thing: if you ignore my comment about *not* using `xcmsRaw`, the following works: ``` xr

The xcms:multipleTerms annotation is not a limitation of EDAM. bio.tools or Workflowhub or the Bioschemas-beefed-up xcms Vignette could (untested!) allow to annotate a list of EDAM terms . Yours, Steffen

Hi, xcms now has included the Spectra changes, and this PR should now go towards xcms devel branch. Norman and I actually just checked, and there would be no merge...

Hi, currently there is no such parameter. Would it work to filter the resulting peaks ? What is the actual use case ? If there are contaminants, you probably don't...

Hi, could you link any other issue you refer to ? Could you give a code snippet that triggered the issue ? Can you run `traceback()` after the error happened...

Thanks Nir for the additional information. Unfortunately I do not have any direct suggestion. There is https://bioconductor.org/packages/release/bioc/vignettes/BiocParallel/inst/doc/Errors_Logs_And_Debugging.pdf and things to try could be adding `sink(NULL, type = "message")` (see 2.1...

Hm, maybe there is a simpler way to get the debug info: ``` bpparam

Hm, if there was a, say, xcms 4.0 that (also) has classes depending on `Spectra` and friends, could the desired function be added to `SpectraVis` and handle the xcms output...

Please do, I was just about to write an eMail to [email protected] Yours, Steffen ``` Dear PLOS team, when looking at two (nearly) random classes of the PLOSTHES: http://bioportal.bioontology.org/ontologies/PLOSTHES?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%233463 http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%238193...