refactor: patially rewrite code to exctract header info

sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

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refactor: patially rewrite code to exctract header info #252

Closed jorainer closed 2 years ago

jorainer commented 2 years ago

Create index list in R instead of C++.
Use size_t instead of int where suitable.
Ensure that correct data types are passed between R and C++.
Use new (own) implementation to extract the acquisition number from the spectrum ID instead of id::translateNativeIDToScanNumber from proteowizard to avoid segfaults on macOS (https://github.com/sneumann/xcms/issues/422).

jorainer commented 2 years ago

This avoids the segfaults on macOS (although pwiz is then stuck at random for a period of time before proceeding - but at least it does no longer break). I haven't tried, but the changes in RcppPwiz should also work on older proteowizard versions.

sneumann commented 2 years ago

Hi, how much of this PR is still relevant ? Yours, Steffen

jorainer commented 2 years ago

I think we can close that. Maybe I'll have another look if we encounter some errors in future.