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I have an R package called ggstatsplot (https://indrajeetpatil.github.io/ggstatsplot/) which relies on a collection of packages that share a few S3 methods between each other. Therefore, every time the package is loaded, the user is bombarded with messages about this issue, which is not useful for the most users.

> library(ggstatsplot)
Registered S3 method overwritten by 'broom.mixed':
  method      from 
  tidy.gamlss broom
Registered S3 methods overwritten by 'car':
  method                          from
  influence.merMod                lme4
  cooks.distance.influence.merMod lme4
  dfbeta.influence.merMod         lme4
  dfbetas.influence.merMod        lme4

Is there something I can implement in the package internally to avoid these messages getting printed to the user's console? Maybe something using .onAttach?

Indrajeet Patil
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    As a user I find these warnings very useful. I wouldn't want to have them suppressed because that would make debugging harder. If a user finds these warnings not useful, they can modify their `options` as described in `help("library")` to switch them off. – Roland May 19 '20 at 07:56

2 Answers2

5

Quickly looked at the code of the package on GitHub, and to me it seems like some of those functions should be removed from NAMESPACE.

You are using @importFrom() however simply adding an "Imports:" declaration in DESCRIPTION and then calling the functions by specifying the namespace, i.e. package::function is enough. This way they would not get attached to the namespace and would not conflict with one another.

Looked a bit closer, and it seems that the issue is with the packages that you export, not your library itself. So for example simply calling library(broom.mixed) produces the conflicts. Since you export some of its import (from broomExtra) the same conflicts appear.

Seems like there is an issue about it already on their GitHub: HERE so best case would be to issue a pull request to them. Or alternatively - maybe you don't really need to export those functions in the first place.

Karolis Koncevičius
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  • I've a similar problem in the `DecomposeR` package [link](https://CRAN.R-project.org/package=DecomposeR); the `check.emd` and `inst.pulse` are respectively using functions from `usethis` and `hht`, themselves importing the `cli` and spatstat.geom` packages, both having a different `print.boxx` method. I tried the `package::function` notation, and removed all the `@importFrom` and `@import` lines, but when I use the two functions in the same script, I still have the warning message. Can't I use the functions of these packages (who do not rely on `print.boxx`) in a way preventing any conflict ? – Sébastien Wouters Nov 08 '21 at 11:53
4

Therefore, every time the package is loaded, the user is bombarded with messages about this issue, which is not useful for the most users.

As a "peace of mind" workaround, users can simply set the environment variable _R_S3_METHOD_REGISTRATION_NOTE_OVERWRITES_ to one of 0, no or false before loading any of the affected packages:

Sys.setenv(`_R_S3_METHOD_REGISTRATION_NOTE_OVERWRITES_` = "false")

Background: There was some instructive conversation about overwriting S3 methods becoming verbose with R 3.6 over at rlang's GitHub repo for anyone interested in more details.

Salim B
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  • This works, however I have to use it every time I restart Rstudio. Is there a way to make this permanent? – mat Feb 24 '21 at 08:17
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    Add the line to your [`.Rprofile`](https://support.rstudio.com/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf) file. – Salim B Feb 24 '21 at 15:02