Ville Koskinen

I appreciate this is a niche use case, but we build and ship relocatable Perl as part of a product. I'm building Perl 5.38 and we currently use: ``` ./Configure...

As I understand, -Dprefix sets the runtime path while DESTDIR is just for copying files to a target path. I just tried using -Dprefix=... to see if it works: ```...

Thank you for considering it! Any way to signal the error is fine as long as it's in the MS2PIPFeatureGenerator documentation.

When a spectral library is searched, there are two fragment tolerances to consider: the user specifies the tolerance of the input data, and something must specify the tolerance of peaks...

I'm glad to see chimeric spectra taken into account. What about intact crosslinked peptides, e.g. disulfide bonds, or looplinked or cyclic peptides? Protein-level data is inherently problematic in a peptide-centric...

It will be a while before I can test the latest version, sorry.

There is actually debug logging that is almost sufficient for what I was looking for. I've done: ``` logging.getLogger('ms2rescore.feature_generators.deeplc').setLevel(logging.DEBUG) logging.getLogger('deeplc.deeplc').setLevel(logging.DEBUG) logging.getLogger('ms2rescore.feature_generators.ms2pip').setLevel(logging.DEBUG) logging.getLogger('ms2pip.core').setLevel(logging.DEBUG) ``` And this gives sufficient progress messages from...

Yes, that solves it for the header file path. (I can't see how changing `INC => $INCLUDE` to `INC => undef` has fixed it, though! In both cases INC is...

I agree it's a niche use case. Before submitting this bug report, I edited Makefile.PL locally and did almost exactly what you describe: push the additional linker argument to `@libs`....

It may help to refer to https://www.matrixscience.com/help/data_file_help.html#PARAMS: PEPMASS is peptide mass "optionally followed by intensity and charge". Positive and negative charge states are specified as "N- to N+ where N...