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[Bioc-devel] Vignettes location in BiocCheck vs R CMD check

6 messages · Martin Morgan, Diego Morais, Armen Abnousi +1 more

Original
Armen Abnousi
# 
Hi,

I'm trying to submit my first package. but I'm confused about the location
of the vignettes in my submitted package. It seems like BiocCheck is
expecting the vignettes to go in <packagename>/vignettes directory but R
3.2+ expects them to go in <packagename>/inst/doc directory. Wherever I put
them, one of the checks complains about their location. Can't put them in
both directories either.

Thanks,
Armen
Martin Morgan
#
On 01/29/2018 02:41 PM, Armen Abnousi wrote:
For Bioconductor, only include the _source_ of your vignette. Include 
the source in the vignettes/ directory.

When your package is configured correctly, R CMD build <YourPackage> 
will build your vignette and create the inst/doc/ tree containing the 
built vignette products. R CMD check <YourPackage>.tar.gz will check the 
built product, and be happy.

There might be complaints if, for instance, your vignette is not 
configured correctly, so R CMD build does not build it.

Martin
This email message may contain legally privileged and/or...{{dropped:2}}
Diego Morais
# 
Hello, Armen.

Your vignettes should be located in <packagename> / vignettes. The vignette
will be built automatically later.

2018-01-29 16:41 GMT-03:00 Armen Abnousi <a.abnousi at gmail.com>:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Armen Abnousi
    

    

      
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Thanks for your answers, that helped but now there is another issue. The
vignette in vignettes/ directory is referring to a bib file for references.
The bib file is in the inst/ directory (so I have used
../inst/REFERENCES.bib) to point to it. I don't get any warnings on my
Linux computer when running check and BiocCheck. But when I submit the
package it builds on Mac OS with no errors but on Linux it gives the error

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called bibtex

Is this related to my referencing to the bib file? How could I solve this
issue. I appreciate your help.

Thanks!

On Mon, Jan 29, 2018 at 11:49 AM, Diego Morais <arthur.vinx at gmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kasper Daniel Hansen
    

    

      
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Put the bib file in /vignettes.  Perhaps see a couple of packages for
examples, including how to use BiocStyle

        
On Mon, Jan 29, 2018 at 3:26 PM, Armen Abnousi <a.abnousi at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Armen Abnousi
    

    

      
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Thanks! I ended up putting the references in the YAML rather than as a
separate bib file.

On Mon, Jan 29, 2018 at 5:27 PM, Kasper Daniel Hansen <

        
kasperdanielhansen at gmail.com> wrote: