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rickhelmus / patRoon

Workflow solutions for mass-spectrometry based non-target analysis.
https://rickhelmus.github.io/patRoon/
GNU General Public License v3.0
65 stars 19 forks source link

MetaClean package deprecated #81

Closed tsufz closed 11 months ago

tsufz commented 1 year ago

Hi Rick, The MetaClean package was deprecated some while ago (as it's dependencies scmamp and fastADAboost) as they are stalled for some while (several years). Thus, for a non experienced user, it is impossible to compile all the sources and to install patRoon properly. Please consider removing the dependency on MetaClean.

Yours Tobias

rickhelmus commented 1 year ago

Hi Tobias,

Thanks for the heads-up! I did notice that fastADABoost was removed, as a work around you can either install it from GitHub or MRAN, e.g. this is what I do with CI

remotes::install_github("souravc83/fastAdaboost")
install.packages('fastAdaboost', repos = 'https://mran.revolutionanalytics.com/snapshot/2022-07-01')

My hope was that fastADABoost would come back, but that doesn't seem to be the case as you mentioned.

I didn't notice scmamp though, will check that out.

Note that MetaClean is an optional dependency, so it shouldn't cause issues for the patRoon installation. In any case, I will upload the documentation for this.

tsufz commented 1 year ago

Hi Rick, Yes, thanks for the update!

Best Tobias

rickhelmus commented 11 months ago

The new installation procedure/docs handle this better now, so I think this can be closed.