[R-pkg-devel] Unneeded S3 method registration

[Lenth, Russell V]

Dear R package developers

My emmeans package failed preliminary checks when I submitted an update today, apparently due to a recent change in requirements on method registration. The message I got was:

* checking S3 generic/method consistency ... NOTE
Apparent methods for exported generics not registered:
  emm_basis.Gam emm_basis.MCMCglmm emm_basis.averaging
  emm_basis.betareg emm_basis.brmsfit emm_basis.carbayes emm_basis.clm
  emm_basis.clmm emm_basis.coxme emm_basis.coxph emm_basis.default
  emm_basis.gam emm_basis.gamlss emm_basis.gamm emm_basis.gee
  emm_basis.geeglm emm_basis.geese emm_basis.gls emm_basis.gnls
  emm_basis.hurdle emm_basis.lqm emm_basis.lqmm emm_basis.mblogit
  emm_basis.mcmc emm_basis.mcmc.list emm_basis.mira emm_basis.mmer
  emm_basis.multinom emm_basis.nlme emm_basis.nls emm_basis.polr
  emm_basis.qdrg emm_basis.rms emm_basis.rq emm_basis.rqs
  emm_basis.stanreg emm_basis.survreg emm_basis.svyolr
  emm_basis.zeroinfl recover_data.MCMCglmm recover_data.averaging
  recover_data.betareg recover_data.brmsfit recover_data.carbayes
  recover_data.clm recover_data.clmm recover_data.coxme
  recover_data.coxph recover_data.default recover_data.gam
  recover_data.gamlss recover_data.gamm recover_data.gee
  recover_data.geeglm recover_data.geese recover_data.gls
  recover_data.gnls recover_data.hurdle recover_data.lqm
  recover_data.lqmm recover_data.manova recover_data.mblogit
  recover_data.mcmc recover_data.mcmc.list recover_data.mira
  recover_data.mmer recover_data.multinom recover_data.nlme
  recover_data.nls recover_data.polr recover_data.qdrg recover_data.rms
  recover_data.rq recover_data.rqs recover_data.stanreg
  recover_data.survreg recover_data.svyglm recover_data.svyolr
  recover_data.zeroinfl
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.

I guess my question is "why does this matter?" There are many, many functions mentioned here, but they are all methods for emm_basis and recover_data. Both generics are in the emmeans namespace, as are all these functions.

The section on registering S3 methods explains:

> The standard method for S3-style UseMethod dispatching might fail to locate methods defined in a package that is imported but not attached to the search path. To ensure that these methods are available the packages defining the methods should ensure that the generics are imported and register the methods using S3method directives...

But clearly all those methods flagged in the messages will be found in the same namespace as the generics -- emm_basis and recover_data -- so not being able to find them is not an issue. Moreover, emm_basis() and recover_data() are not meant to be called directly by a user, or even by code in another package. They are only meant to be called within the function emmeans::ref_grid(), and the existence of those generics and methods is simply a mechanism for being able to support a lot of different model classes.

Obviously, I could add a whole lot of S3method() directives to the NAMESPACE file, but it just seems wasteful to export all those methods when they are never needed outside the emmeans namespace.

Am I missing something?

Thanks

Russ Lenth



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