Johannes Rainer

or implement an additional `reconstructFeatureSpectra` that does take correlation of the peaks across samples into account.

If you are too busy @michaelwitting I can implement the function to reconstruct the MS2 spectrum (#377) and let you have a look at it if it makes sense. Once...

BTW, if not mistaken you said you were working on the swath vignette @michaelwitting - if so, can you push or make a pull request?

For the things that are still missing - I'm also quite busy at present, but we could discuss and implement the things at latest in Den Haag.

Please provide also the output from `sessionInfo()`

Note that the problem reported in https://github.com/Bioconductor/BiocParallel/issues/177#issuecomment-1055586237 does not apply here, since we're opening the file in each parallel process. To reproduce and better understand the error, can you please...

maybe you had already the variable `filteredMs2Spectra_NEG` in your R session (from a previous analysis)? I don't see any possibility results to be different whether you run the `featureSpectra` with...

Hm, also for the gap-filling, I can not explain why that should be any different if run in parallel or serial processing mode. Note that gap filling will not have...

Thanks for reporting! `xcms` does not create any temporary files, so I guess it must be related to R. Could it be that in the time course of this 2...

I got the same errors recently while processing large experiments - and this was related to the system running out of memory (64GB memory, 6 cores; in fact I did...