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[R-pkg-devel] Etiquette for package submissions that do not automatically pass checks?

6 messages · Voeten, C.C., Duncan Murdoch, Joshua Ulrich +1 more

Original
Voeten, C.C.
# 
A while ago, I submitted an update to my package 'buildmer' that does not pass R CMD check. This is deliberate. The package contains functionality to run on cluster nodes that were set up by the user and needs to access its own internal functions from there. In previous versions of the package, I had maintained a list of those functions and clusterExport()ed them, but that had the side effect of overwriting any same-named user objects on the user-provided cluster nodes, which I thought was poor form. The update therefore accesses these functions using ':::', which triggers a check warning.

I thought the etiquette was to explain this in the 'Comments' box when submitting, but this gave me the same automated message that the package does not pass checks and that I should fix it or reply-all and explain. This led me to believe that I should not have used the 'Comments' box for this purpose, hence I resubmitted the package leaving the comments box empty, and I replied-all to the subsequent e-mail I got with an explanation similar to the above.

It has now been a while since I sent that e-mail (ten days), and I have yet to hear back. I was wondering if the message had gotten lost, if they simply haven't gotten around to it yet (I have no idea how much mail they receive on a daily basis, but I'd think it's a lot more than I do), or if I should have handled this differently. Only CRAN can answer the first two questions, but before I bother them: was this the correct procedure, or should I simply have done something differently?

Thanks,
Cesko
Duncan Murdoch
#
On 14/08/2020 3:08 p.m., Cesko Voeten wrote:
It seems to me that what you should have done is "reply-all and 
explain", as the automated message said.
You can see the state of your submission using the foghorn package. 
cran_incoming("buildmer") currently shows your package is in the 
"archive", which means "package rejected: it does not pass the checks 
cleanly and the problems are unlikely to be false positives".

I only see version 1.7 there, which may indicate that you resubmitted 
exactly the same package (down to the version number).  As the 
instructions at 
https://cran.r-project.org/web/packages/policies.html#Re_002dsubmission 
say, "Increasing the version number at each submission reduces confusion 
so is preferred even when a previous submission was not accepted."

What I'd suggest now is that you do nothing more for a day or two, 
because CRAN members who aren't on holiday might read and respond to 
your message.  If you don't hear anything, then I'd start over again, 
with a new version number, and an explanation in the comments, and 
likely a followup reply-all.

Alternatively, you could export those troublesome functions from your 
package but document them as for internal use only.  Renaming them with 
a name starting with "." will make them harder for users to stumble 
upon, but you can still access them using buildmer::.something, you 
shouldn't need clusterExport(). Then you will meet the technical 
requirement and not need any explanation.

Duncan Murdoch
Joshua Ulrich
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On Fri, Aug 14, 2020 at 2:54 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
You have more than a few days.  As it says on CRAN:
"CRAN submission is offline from Aug 14 to Aug 24, 2020 (CRAN team
vacation and maintainance work)"

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Voeten, C.C.
    

    

      
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Duncan, Joshua,

Thanks for the feedback. I had indeed forgotten to increment the version number, so that may explain it. I'll give it until a few days after the 24th, and then just resubmit with a new version number.

Also, thanks for introducing me to the foghorn package, I wasn't aware of it before.

Best,
Cesko

Op 14-08-2020 om 22:31 schreef Joshua Ulrich:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Ivan Krylov
    

    

      
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Dear Cesko,

On Fri, 14 Aug 2020 21:08:55 +0200

        
Cesko Voeten <c.c.voeten at hum.leidenuniv.nl> wrote:

        

            

      
      
      
    

        
Apologies for derailing the thread, but I had a similar problem a few
months ago [*], found what looks like a different solution but did not
have time to investigate it further.

Given that serialize() does not send package namespaces over the wire
[**], why would it be a bad idea to pass actual functions (instead of
character strings naming functions) to parallel::parLapply and friends?
This seems to avoid the need to export the worker functions or use :::
in calls to parallel functions from package functions. Unless I am
missing something, which I probably am.

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Voeten, C.C.
    

    

      
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Dear Ivan,

            

      
      
      
    

        
No worries, these issues are also what this mailing list is for! I've meanwhile heard back from Uwe that I should resubmit after the 24th, and that he still would like the warning to go away. Your suggestion certainly makes sense, but it would require a rewrite of some delicate parts. Fortunately, I was already passing a parameter list around anyway, so I can just add those functions in that list, and I'll probably end up indeed taking that approach. Thank you for the suggestion! It does feel like an awful hack, though, given that the language supports doing this in a clean way using the ::: operator. But I also understand that CRAN want to impose certain limitations to discourage bad practices, and I trust their judgment that ::: is one of those.

Best,
Cesko