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[Bioc-devel] Package checks with WARNING

5 messages · Lapuente Santana, Oscar, Shepherd, Lori, Hervé Pagès

Lapuente Santana, Oscar
# 
Dear Bioconductor developers/maintainers,

My package ?easier? checks with WARNING in both the current 3.15 release and the devel version.
I am just checking in to see if that?s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency)

Thanks in advance,
Cheers, ?scar
Shepherd, Lori
# 
Ideally all warnings and notes would be addressed. However as long as the package currently is not in an ERROR or TIMEOUT state this is okay; especially if it comes from a dependency of a dependency.
Please keep an eye on all warnings and make sure there is not anything new or anything that can (and then should) be addressed.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Hervé Pagès
# 
Hi ?scar,
On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote:

            

      
      
      
    

        
Sure but you can get rid of it by importing only what you need from the 
coin package. Right now you import the full coin namespace, by having 
import(coin) in your NAMESPACE file, and that introduces a clash with 
importFrom(rstatix,wilcox_test) that you also have in there.

I'm actually not sure what you need coin for (I was not able to find a 
place in your code where you make any use of it). So maybe you could 
just drop that dependency entirely?

Best,

H.

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Lapuente Santana, Oscar
    

    

      
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Hi Herv?,

Thanks for your suggestion. 

The package rstatix which I used and it's set as an import, calls the coin package but this one is defined as a suggests in the description file of rstatix package (https://github.com/kassambara/rstatix/blob/master/DESCRIPTION). 

In particular, I am calling two two functions from this package: rstatix::wilcox_test and rstatix::wilcox_effsize. The later uses several functions from the coin package and one is called the same way which is coin::wilcox_test and then the warning arises.
 
Given this situation, I would feel more comfortable importing the full coin package. What are your thoughts?

Cheers, ?scar

        
?On 12/10/2022, 20:07, "Herv? Pag?s" <hpages.on.github at gmail.com> wrote:

        
Hi ?scar,

        
On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote:

        
> Dear Bioconductor developers/maintainers,
    >
    > My package ?easier? checks with WARNING in both the current 3.15 release and the devel version.
    > I am just checking in to see if that?s okay since this was also the case in the first submission (the warning stems from a dependency of a dependency)

    Sure but you can get rid of it by importing only what you need from the 
    coin package. Right now you import the full coin namespace, by having 
    import(coin) in your NAMESPACE file, and that introduces a clash with 
    importFrom(rstatix,wilcox_test) that you also have in there.

    I'm actually not sure what you need coin for (I was not able to find a 
    place in your code where you make any use of it). So maybe you could 
    just drop that dependency entirely?

    Best,

    H.

    >
    > Thanks in advance,
    > Cheers, ?scar
    >
    > 	[[alternative HTML version deleted]]
    >
    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&amp;data=05%7C01%7C%7Cb6a12862a3d34c6fc57608daac7c93b1%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C0%7C638011948302682925%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=zX2HiEuNhlfF8IQ1N61wbAyt1Sd2k4hiVISTMJXA3qk%3D&amp;reserved=0

    -- 
    Herv? Pag?s

    Bioconductor Core Team
    hpages.on.github at gmail.com

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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On 12/10/2022 13:42, Lapuente Santana, Oscar wrote:

        

            

      
      
      
    

        
I see. But still, you're only supposed to import what your code uses 
_directly_. In this case your code doesn't make any call to coin or 
doesn't use any symbol defined in coin. The code in rstatix does, but 
not your code.

One concern is that you want to make sure that coin is installed on the 
user machine, so it needs to be listed as a dependency. One way to 
achieve this is to move coin to Depends, and to not import anything from 
it. I just tried this but R CMD check now produces:

 ? * checking dependencies in R code ... NOTE
 ? Package in Depends field not imported from: ?coin?
 ? ? These packages need to be imported from (in the NAMESPACE file)
 ? ? for when this namespace is loaded but not attached.

IMO this is actually a legitimate use of Depends, so I'd say it's ok. At 
least now you get a NOTE instead of a WARNING ;-)

A more hacky solution is to keep coin in Imports and to import an 
arbitrary symbol from it. Could be anything, except 'wilcox_test' of 
course, to avoid the clash with importFrom(rstatix,wilcox_test). That 
should produce a clean R CMD check.

Hope this helps,

H.