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[Bioc-devel] Warnings on R CMD check on Mac OS and Linux

7 messages · Nitesh Turaga, Oluwafemi OLUSOJI, Hervé Pagès

Original
Oluwafemi OLUSOJI
# 
Dear All,

I get this warning on the latest update of my package. The warning occurs
only with Mac and Linux. I am a bit at loss here. These errors don't
actually exist because these functions and methods are properly documented.
The missing link doesn't even exist anymore.

I have rebuilt both the documentation and rebuilt the source. R CMD check
and R CMS check --as.cran doesn't report either on my system as well. I
will appreciate any heads-up here.

Regards,
Daniel


Missing link or links in documentation object 'oneDgate.Rd':
  getChannel

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  PhytoFilter clusterExtract clusterExtractp debrisNc
  getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
  reducedFlowframe rowNumbers summaries
Undocumented S4 methods:
  generic 'summaries' and siglist 'DebrisFilter'
  generic 'summaries' and siglist 'MarginEvents'
  generic 'summaries' and siglist 'PhytoFilter'
Nitesh Turaga
# 
Hi

We can help you better if you tell us which package you are talking about ?

Best,

Nitesh 

?On 3/8/21, 5:46 PM, "Bioc-devel on behalf of Oluwafemi OLUSOJI via Bioc-devel" <bioc-devel-bounces at r-project.org on behalf of bioc-devel at r-project.org> wrote:

    Dear All,

    I get this warning on the latest update of my package. The warning occurs
    only with Mac and Linux. I am a bit at loss here. These errors don't
    actually exist because these functions and methods are properly documented.
    The missing link doesn't even exist anymore.

    I have rebuilt both the documentation and rebuilt the source. R CMD check
    and R CMS check --as.cran doesn't report either on my system as well. I
    will appreciate any heads-up here.

    Regards,
    Daniel


    Missing link or links in documentation object 'oneDgate.Rd':
      getChannel

    See section 'Cross-references' in the 'Writing R Extensions' manual.
    * checking for missing documentation entries ... WARNING
    Undocumented code objects:
      PhytoFilter clusterExtract clusterExtractp debrisNc
      getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
      reducedFlowframe rowNumbers summaries
    Undocumented S4 methods:
      generic 'summaries' and siglist 'DebrisFilter'
      generic 'summaries' and siglist 'MarginEvents'
      generic 'summaries' and siglist 'PhytoFilter'


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    Bioc-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel
Oluwafemi OLUSOJI
# 
Hello,

It is a package I recently submitted, cyaniFilter.

Thank you for the prompt response.

Regards,
Daniel
On Tue, Mar 9, 2021, 00:09 Nitesh Turaga <nturaga.bioc at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Hi,

I don't see that you have aliases for these symbols, hence the warning:

   hpages at spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
   hpages at spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd
   etc...

Note that even though you have aliases for some PhytoFilter **methods**:

   hpages at spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep 
alias | grep method
 
fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
   plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
 
reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}


here 'R CMD check' is complaining about the lack of an alias for the 
PhytoFilter **object** (which turns out to be a function). Since you 
export this symbol (via the export(PhytoFilter) directive in your 
NAMESPACE file), you need to provide an alias for it in one of your man 
pages.

Hope this helps,

H.

        
On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Oluwafemi OLUSOJI
    

    

      
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Hello Herve,

Thank you for the insight, but after rewriting the man pages by hand. I
still get the same error after the latest commit. I am really at a loss
here because this builds perfectly on my system.

Regards,
Daniel

Op do 11 mrt. 2021 om 03:11 schreef Herv? Pag?s <hpages.on.github at gmail.com

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Oluwafemi OLUSOJI
    

    

      
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Hello Herves,

I finally solved this. It had more to do with my commits than the package
itself.

There is this error message when the package is built on a Windows server.
What am I to do about this?

Regards,
Daniel

===============================

 R CMD BUILD

===============================

* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
ERROR: dependency 'flowCore' is not available for package 'cyanoFilter'
* removing 'C:/Users/pkgbuild/AppData/Local/Temp/RtmpYhB4xB/Rinst1ce0655031d2/cyanoFilter'
      -----------------------------------
ERROR: package installation failed


Op do 11 mrt. 2021 om 15:54 schreef Oluwafemi OLUSOJI <
oluwafemi.olusoji at uhasselt.be>:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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On 3/11/21 7:45 AM, Oluwafemi OLUSOJI wrote:

            

      
      
      
    

        
The flowCore package cannot currently be installed because it requires 
cytolib >= 2.3.4 which doesn't compile on Windows at the moment. The 
cytolib maintainers are aware of the situation and working on it.

Not much we can do so let's ignore for now.

Thanks,
H.