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It seems that if a common 'error' is encountered for each spectrum, then this will flood the console with one message per spectrum (which for MSI Data is a lot!) eventually leading to a system crash. The error for the dataset linked above is given below. Perhaps it would be possible to just display the warning once per dataset, rather than per spectrum?
- Warning in .createMassObject(mass = mass, intensity = intensity, metaData = m, :- According to the metadata information the imported data are centroided, but they are treated as profile (MassSpectrum) data. Maybe you want to use 'centroided=TRUE'. See '?import' for details.
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I see your point. I could remove the immediate. argument but than it is not clear for which spectrum the warning was thrown. You are right that for imzML datasets a collected warning once per dataset would be more helpful but for other datasets every spectrum could contain different errors.
Does suppressWarnings(importImzMl(file)) works for you?
I have been evaluating multiple imzML parsers (see here https://imzml.github.io/) with publicly available imzML datasets (e.g. https://metaspace2020.eu/datasets?ds=2017-06-30_07h26m26s) and experienced some issues with MALDIquantForeign.
It seems that if a common 'error' is encountered for each spectrum, then this will flood the console with one message per spectrum (which for MSI Data is a lot!) eventually leading to a system crash. The error for the dataset linked above is given below. Perhaps it would be possible to just display the warning once per dataset, rather than per spectrum?
The text was updated successfully, but these errors were encountered: