search

mark-andrews / psyntur

Tools to help teach data analysis using R to NTU Psychology students
Other
5 stars 2 forks source link

Remove GGally import message #28

Open mark-andrews opened 3 years ago

mark-andrews commented 3 years ago

On load of package, we get this:

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

I presume we can avoid this if GGally is not loaded but used via GGally::

jensroes commented 3 years ago

To silence loading messages we can also do suppressMessages(library(GGally)) but defining the name space is good too.

mark-andrews commented 3 years ago

The Wickham, who can not be wrong about anything ever, says one must always use the namespaced functions in R code in R packages. So e.g. we would do 

GGally::ggairs ...

on https://github.com/mark-andrews/psyntur/blob/10319a588cda8e7b56da5f31ba12b8d11c99cfd7/R/visualization-utils.R#L256 and so on elsewhere. Actually, this makes tidyverse and ggplot code quite verbose, as you have to use the namespace for every function, but it is safer to use generally.

jensroes commented 3 years ago

Is the reason to avoid masking issues? I can see how it is saver to use the name space.

mark-andrews commented 3 years ago

Yes, it is too avoid masking. Here's a reading from the Book of Wickham: https://r-pkgs.org/namespace.html

mark-andrews commented 3 years ago

This apparently is not easy to fix. Using the :: approach does not solve it it seems. When GGally code runs, it itself does a library command that triggers it. See https://stackoverflow.com/questions/67356592/registered-s3-method-overwritten-by-ggally-method-from-gg-rstudio-loading

We also can't resort to suppressMessages as the imports in psyntur are not issued by library commands but by the import commands in NAMESPACE, which are auto generated and can't be wrapped by suppressMessages.

There is talk about solving this upstream, either in ggplot2 or GGally, see https://github.com/ggobi/ggally/issues/292. I will leave it to them to solve it. In the meantime, we will leave this as is, which is annoying :(.

mark-andrews commented 3 years ago

I am re-opening this issue because we need this problem to go away ultimately as it creates a spurious warning that will distract users. Basically, every time we do library(psyntur), we get this warning/message and it seems impossible to suppress internally in the psyntur package. I still don't know fully who is responsible for this message, GGally or ggplot2, or if there is some fix to it, but it is a really annoying message. It is bad for my mental well-being, and bad for the mental well-being of all psyntur users.