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S4 class name conflicts

4 messages · Michael Lawrence, Gábor Csárdi

Original
Gábor Csárdi
# 
The RNeXML CRAN package currently has some check warnings, originating
from an S4 class name conflict.

RNeXML sets the S4 class "tree". A dependency of the package now
depends on the cli package, which calls setOldClass() on an S3 "tree"
class.

This causes two potential issues. One is that RNeXML maybe ends up
using cli's class internally, because this is what we see at install
time:

** byte-compile and prepare package for lazy loading
Found more than one class "tree" in cache; using the first, from namespace 'cli'
Also defined by ?RNeXML?

The second issue is an error when RNeXML is unloaded:

? unloadNamespace("RNeXML")
Error in .mergeMethodsTable(generic, mtable, tt, attach) :
  trying to get slot "defined" from an object of a basic class
("environment") with no slots

This makes R CMD check fail as well.

Is cli doing something wrong here? Or is this a bug in base R? Or is
it a known limitation? If the latter, would it make sense for the
RNeXML installation to fail instead of creating a broken package. (If
it is a broken package at all.)

Gabor
Michael Lawrence
# 
Hi Gabor,

Thanks for reporting this issue. Would you be able to help me
reproduce it? I'm guessing this depends on some combination of git
checkouts, so it would be helpful to know which.

Michael
On Tue, Feb 8, 2022 at 6:32 AM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Gábor Csárdi
    

    

      
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Hi Michael,

you only need the CRAN versions. You probably need a recent version of
pillar, to
create the name conflict with its dependency:

install.packages("pillar")
install.packages("cli")
install.packages("RNeXML", type = "source")

This will already give you:
** byte-compile and prepare package for lazy loading
Found more than one class "tree" in cache; using the first, from namespace 'cli'
Also defined by ?RNeXML?

and then:

library(RNeXML)
unloadNamespace("RNeXML")

Error in .mergeMethodsTable(generic, mtable, tt, attach) :
  trying to get slot "defined" from an object of a basic class
("environment") with no slots

This is macOS arm64, but looking at the CRAN check page, that should not matter.

Let me know if this does not work, and the I'll create a Docker
container or something more reproducible.

Thanks,
Gabor

On Tue, Feb 8, 2022 at 5:53 PM Michael Lawrence

        
<lawrence.michael at gene.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Michael Lawrence
    

    

      
      #
    

  


  

      
Great, thanks. I have fixed both issues and will commit after more testing.

Michael

        
On Tue, Feb 8, 2022 at 9:07 AM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote: