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MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html
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Remove `alternateAnalyze.R` functions? #325

Open meowcat opened 1 year ago

meowcat commented 1 year ago

Are the functions in alternateAnalyze.R in active use? Those were originally implemented by ermueller 8 years ago and small touches were done by treutler later.

L167 references an occurrenceMatrix that doesn't point to anything I know.

analyzeMsMs.formula.optimized is used by analyzeMsMs.optimized is used by newStep2WorkFlow is used in validateMassBank.R -> .unitTestRMB2. This is not called from anywhere currently, and other than that I am not aware of any use of newStep2WorkFlow. Unless there is a maintainer who takes over alternateAnalyze and figures out what occurrenceMatrix is, I would advocate to remove the functionality (despite probably being more efficient than the original implementation).

@sneumann @tsufz @schymane ?

https://github.com/MassBank/RMassBank/blob/3db8775e6603e15ed433a183d0de6e5b914d1b0e/R/alternateAnalyze.R#L167

tsufz commented 1 year ago

In my patchy memory, I can remember that ermueller worked also on the unit tests. Hence, it is not surprising that the functions are used in .unitTestRMB2. I suggest to deprecate the functions.