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[R-pkg-devel] submitting package update failed, since old version out of date (?)

6 messages · Aisouda Hoshiyar, Georgi Boshnakov, Gábor Csárdi +1 more

Original
Aisouda Hoshiyar
# 
Hi,

submitting an update of our package ordPens failed (update version is 1.0.0), reporting the following:
Version: 1.0.0
ok
Version: 0.3-1
Check: R code for possible problems, Result: NOTE
  genRidge: no visible global function definition for 'plogis'
  ordGene: no visible global function definition for 'anova'
  ordGene: no visible global function definition for 'lm'
  ordSelect: no visible binding for global variable 'sd'
  ordSmooth: no visible binding for global variable 'sd'
  plot.ordPen: no visible global function definition for 'grey'
  plot.ordPen: no visible global function definition for 'devAskNewPage'
  plot.ordPen: no visible global function definition for 'lines'
  predict.ordPen: no visible global function definition for 'plogis'
  Undefined global functions or variables:
    anova devAskNewPage grey lines lm plogis sd
  Consider adding
    importFrom("grDevices", "devAskNewPage", "grey")
    importFrom("graphics", "lines")
    importFrom("stats", "anova", "lm", "plogis", "sd")
  to your NAMESPACE file.
Version: 0.3-1
Check: package dependencies, Result: NOTE
  Package suggested but not available for checking: ?IsoGene?
https://cran.r-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html>

https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/ <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/>

But these are exactly the new changes that we already took care of in the updated version 1.0.0
The previous version 0.3-1 is from 2015 and due to R updates, the old package won?t work any more. 
That is exactly the reason for update version 1.0.0, were everything is fixed now.

Also,
- there is a NOTE about change in maintainer, which is already stated in the cran-comments.md, and the previous maintainer sent an e-main to CRAN as well
- there is a NOTE saying 'Examples with CPU (user + system) or elapsed time > 10s?
which is also stated in the cran-comments.md explaining that cross-validation examples are important for illustrating the package usage.
 

So is this a false positive? 

Best
Aisouda
Georgi Boshnakov
# 
When the previous version has problems, you get an email listing them, followed with something like 'Did you fix them? Please Reply-All...'

Maybe you missed the last phrase?

Georgi Boshnakov



Get Outlook for Android<https://aka.ms/AAb9ysg>
Aisouda Hoshiyar
# 
The CRAN (pretest) email states:
 
package ordPens_1.0.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: 
Debian: <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/00check.log <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/00check.log>>
Status: 2 NOTEs

Last released version's CRAN status: NOTE: 13
See: <https://CRAN.R-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html>>

Please fix all problems and resubmit a fixed version via the webform. 
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

I really don?t understand how else to fix (and what to fix). These are out of date problems of version 0.3-1, which are not relevant any more in version 1.0.0
Version 1.0.0 exactly was a fix to those. 

Do you think I can reply-all & explain that this must be a false-positive?

Best
Aisouda

  
  


  


      

    

    

      
      

        


  

        

      Gábor Csárdi
    

    

      
      #
    

  


  

      
I think they are this:

* checking CRAN incoming feasibility ... NOTE
...

and this:

* checking examples ... [76s/77s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
ordPens-package 54.112  0.044  54.158
ordPCA          18.377  0.004  18.382

G.

On Tue, Aug 17, 2021 at 3:38 PM Aisouda Hoshiyar

        
<aisouda.hoshiyar at hsu-hh.de> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Aisouda Hoshiyar
    

    

      
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* checking CRAN incoming feasibility ... NOTE
Maintainer: ?Aisouda Hoshiyar <aisouda.hoshiyar at hsu-hh.de>?

is just a change of the maintainer and already declared in my cran-comments.md file.

Best
Aisouda

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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But the example timing...:
Please reduce each example to less than 5 sec.

Best,
Uwe Ligges

        
On 17.08.2021 15:53, Aisouda Hoshiyar wrote: