chore: remove R/methods-fragments.R (moved to PSMatch)

[sgibb]

After adapting to the new PSMatch::calculateFragments (with fixed_modifications instead of modifications) some unit tests in topdownr fail. In topdownr MSnbase::calculateFragments overwrites PSMatch::calculateFragments.
Unfortunately the syntax is slightly different, e.g. MSnbase knows nothing about fixed_modifications.

To reproduce this error, load MSnbase before PSMatch:

library("MSnbase")
library("PSMatch")
calculateFragments("AACE", fixed_modifications=NULL)
# Error in .local(sequence, ...) : 
#   unused argument (fixed_modifications = NULL)

MSnbase::calculateFragments's body is similar to PSMatch::calculateFragments's body. The only difference is the verbose = isMsnbaseVerbose() argument/setting.
So maybe it would be useful to remove this file? (or adjust to PSMatch's arguments).

[lgatto]

Indeed. I am surprised that there's still such a function in MSnbase.