warning with R 3.6

[IndrajeetPatil]

With the development version of R 3.6 I am getting the following warning once per session. Is this expected? Wasn't getting any such warning with 3.5, so just wanted to raise this issue before the next release.

Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang

[lionel-]

Ah, interesting, thanks! We just need to remove those methods from ggplot2 once rlang 0.3.0 is on CRAN.

@hadley Seems like overwriting S3 methods has finally become verbose.

[IndrajeetPatil]

Until this is implemented, what can I do so that my package won't clutter the terminal with all these messages (I am getting similar things from dplyr, skimr, etc.) when it is loaded?

[lionel-]

What similar thing are you getting from dplyr?

This is not high priority because R 3.6 is still a long ways from being released.

[IndrajeetPatil]

For dplyr, I am getting:

Registered S3 method overwritten by 'dplyr':
  method               from  
  as.data.frame.tbl_df tibble

Completely understandable that this is not a high priority. But I'd still like to not have these messages on my local system with 3.6.0 because they also appear in vignettes, etc. That's why I was asking if there is any temporary workaround to this (like suppressPackageStartupMessages()).

[lionel-]

These are messages so you can use suppressMessages() to muffle them.

[IndrajeetPatil]

But in the context of a package where can I add suppressMessage()?

So, for example, this is what I get with devtools::check(), and this is what the user going to see as well when they do library(ggstatsplot)-

==> devtools::check(args = c('--as-cran'))

Updating ggstatsplot documentation
Writing NAMESPACE
Loading ggstatsplot
Registered S3 method overwritten by 'dplyr':
  method               from  
  as.data.frame.tbl_df tibble
Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Registered S3 method overwritten by 'skimr':
  method      from  
  print.spark pillar
Writing NAMESPACE

[lionel-]

You can use it like this: suppressMessages(library("mypkg")) (though note the messages are triggered on load, not attach, so the suppressMessages might have to be used earlier or might not be practical).

Your users are not going to see the messages because we'll fix them before R 3.6 is out.

[IndrajeetPatil]

Ah, fair point! Thank you very much.

[IndrajeetPatil]

Since the release of ggplot2 3.1.1 I am getting these warnings again. Did something change in the new release?

library(rlang)
library(ggplot2)
#> Registered S3 methods overwritten by 'ggplot2':
#>   method         from 
#>   [.quosures     rlang
#>   c.quosures     rlang
#>   print.quosures rlang

^{Created on 2019-04-10 by the reprex package (v0.2.1.9000)}

Session info

devtools::session_info()
#> - Session info ----------------------------------------------------------
#>  setting  value                                    
#>  version  R version 3.6.0 alpha (2019-03-29 r76300)
#>  os       Windows 10 x64                           
#>  system   x86_64, mingw32                          
#>  ui       RTerm                                    
#>  language (EN)                                     
#>  collate  English_United States.1252               
#>  ctype    English_United States.1252               
#>  tz       America/New_York                         
#>  date     2019-04-10                               
#> 
#> - Packages --------------------------------------------------------------
#>  package     * version    date       lib
#>  assertthat    0.2.1      2019-03-21 [1]
#>  backports     1.1.4      2019-04-10 [1]
#>  callr         3.2.0      2019-03-15 [1]
#>  cli           1.1.0      2019-03-19 [1]
#>  colorspace    1.4-1      2019-03-18 [1]
#>  crayon        1.3.4      2017-09-16 [1]
#>  desc          1.2.0      2019-04-03 [1]
#>  devtools      2.0.2      2019-04-08 [1]
#>  digest        0.6.18     2018-10-10 [1]
#>  dplyr         0.8.0.9009 2019-03-15 [1]
#>  evaluate      0.13       2019-02-12 [1]
#>  fs            1.2.7      2019-03-19 [1]
#>  ggplot2     * 3.1.1      2019-04-07 [1]
#>  glue          1.3.1      2019-03-12 [1]
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#>  munsell       0.5.0      2018-06-12 [1]
#>  pillar        1.3.1      2018-12-15 [1]
#>  pkgbuild      1.0.3      2019-03-20 [1]
#>  pkgconfig     2.0.2      2018-08-16 [1]
#>  pkgload       1.0.2      2018-10-29 [1]
#>  plyr          1.8.4      2016-06-08 [1]
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#>  remotes       2.0.4      2019-04-10 [1]
#>  rlang       * 0.3.4      2019-04-07 [1]
#>  rmarkdown     1.12.3     2019-03-25 [1]
#>  rprojroot     1.3-2      2018-01-03 [1]
#>  scales        1.0.0      2018-08-09 [1]
#>  sessioninfo   1.1.1      2018-11-05 [1]
#>  stringi       1.4.3      2019-03-12 [1]
#>  stringr       1.4.0      2019-02-10 [1]
#>  testthat      2.0.1      2018-10-13 [1]
#>  tibble        2.1.1      2019-03-16 [1]
#>  tidyselect    0.2.5      2018-10-11 [1]
#>  usethis       1.5.0      2019-04-07 [1]
#>  withr         2.1.2      2018-03-15 [1]
#>  xfun          0.6        2019-04-02 [1]
#>  yaml          2.2.0      2018-07-25 [1]
#>  source                            
#>  CRAN (R 3.6.0)                    
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#>  CRAN (R 3.6.0)                    
#>  CRAN (R 3.6.0)                    
#>  CRAN (R 3.5.1)                    
#>  Github (r-lib/desc@c860e7b)       
#>  CRAN (R 3.6.0)                    
#>  CRAN (R 3.5.1)                    
#>  Github (tidyverse/dplyr@df735d1)  
#>  CRAN (R 3.6.0)                    
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#>  Github (yihui/knitr@6103edd)      
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#> 
#> [1] C:/Users/inp099/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.0alpha/library

[lionel-]

They might have released off-branch.

[mjsteinbaugh]

+1 that I'm seeing these messages pop up again on R 3.6.
I have ggplot2 3.3.1 and rlang 0.3.4 installed.

[lionel-]

This is a ggplot2 issue.

[krlmlr]

Not a solution, but still perhaps helpful: the messages can be muted by setting the _R_S3_METHOD_REGISTRATION_NOTE_OVERWRITES_ environment variable to 0: https://github.com/wch/r-source/blob/2caeaf151293da51c38ccc65ff3b02171726a958/src/library/base/R/namespace.R#L1694 .

[GeraldCNelson]

I'm getting similar messages with mailR when I run library(mailR). mailR version is 0.6 The details are
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3

[lionel-]

@GeraldCNelson This is purely between the R.oo and R.methodsS3 packages.

[GeraldCNelson]

This may be true for this particular example with R.oo and R.methodsS3, but it seems like most of the packages I run now have this same message. Here's one for Rselenium.

library(RSelenium)
Registered S3 method overwritten by 'openssl':
  method      from
  print.bytes Rcpp

[lionel-]

This is because these packages don't prefix their class with the package name (e.g. "Rcpp_bytes") so there are collisions when they register methods for third party generics like print().

If we were writing rlang now, we'd use "rlang_quosure" instead of just "quosure" to avoid this kind of issues.

[GeraldCNelson]

What process should we (I) follow to get rid of these?

1. live with it?
2. request package authors to prefix their class with the package name?
3. Something else?

Is there any way to send out a message to all the relevant authors to revise their packages as you suggested?

[lionel-]

2 would be ideal but this might be a highly breaking change as all methods written by downstream packages will need to be renamed as well.

[GeraldCNelson]

Is this something that could be fixed in R3.6.1. It seems like the change that created these messages was made in R3.6. I suppose though that the messages will prompt enough issue reports to authors that they will make the changes. Can you suggest some language to put in an issue report on GitHub for those of us who don't really understand the problem?

[lionel-]

There were always collisions, they just were silent. So I don't think R should remove the message.

I would say something like this:

It seems the class "foo" of your package is conflicting with the same class "foo" of package {bar}, at least for methods baz() and quux(). Since S3 classes are not namespaced, manual namespacing is required to avoid this sort of collisions. Would there be any chance either of you could rename your class to use your package name as a prefix? It probably makes sense to do this renaming in the package with the fewest reverse dependencies, to minimise breakages.

[GeraldCNelson]

I figured that was the case. Thanks for the text to nudge package authors with!

[Narendra-IITRopar]

I am getting a similar message with ez on R 3.6.0

Registered S3 methods overwritten by 'lme4': method from cooks.distance.influence.merMod car influence.merMod car dfbeta.influence.merMod car dfbetas.influence.merMod car

[IndrajeetPatil]

This has nothing to do with rlang and everything to do with lme4.

There is already issue at lmr4 repo about this:
lme4/lme4#510

[rvlenth]

I have noted that if I have the code

if (requireNamespace("ggplot2", quietly = TRUE)) {
    ...
}

then the messages shown in the first comment on this thread appear. However, quietly = TRUE is supposed to suppress all progress and error messages, according to the documentation. It seems to me that S3 method overwrites should also be quieted.

[lionel-]

quietly should only quiet messages intended for the user and providing information about normal behaviour. This is not the case here, the behaviour is faulty and the message is intended for developers. It shouldn't be suppressed.