Johannes Rainer

Could you maybe also provide some information on the system you're running this code (i.e. which OS you use - parallel processing is different on Windows and Unix machines). Ideally,...

The error message you're getting can also mean that the file can not be found. I would suggest the following: inside the loop (i.e. for each parallel process): - check...

The error seems to come from `proteowizard` so there might be some issue with one of your files maybe? Could you try the following: ```r for (f in all_raw_files) {...

Please don't use the *old* functions (`xcmsSet`, `group` etc) anymore. Try to update the workflow to the new functions and objects shown [here](https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html). The first error message *xcmsSource: file not...

Is this issue now solved? Please close if so @wanglai786

The `spectra` returns you all MS1 and/or MS2 spectra from your object. If you're interested in getting all MS2 spectra on an object `xdata` you can use `spectra(filterMsLevel(xdata))`. `featureSpectra` is...

There are two different `combineSpectra` functions, one is in `MSnbase`, that works on `MSpectra` objects, the other is in `Spectra` that works on `Spectra` objects. Thus, it depends on the...

Yes, the function is called `findmzROI`.

On Windows for parallel processing a new R process is started for each parallel job. The error above suggests that somehow one of these R processes was closed or no...

Hm, then maybe there might be some other error which is not reported properly due to the parallel processing. Could you please try the same call but after disabling parallel...