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[Bioc-devel] runnable examples for internal function ?

10 messages · Dan Tenenbaum, Michael Lawrence, Hervé Pagès +2 more

Original
Martin, Tiphaine
# 
Hi,


I would like to know if I need to add a runnable example for each function that has keyword either internal or not.


I ask that because with BiocCheck, version 1.0.2, I had a message for function with keyword "internal" such as "

Checking exported objects have runnable examples...
    * CONSIDER: Adding runnable examples to the following man pages
      which document exported objects:"

and now, I have an error message with BiocCheck, version 1.1.18

* Checking exported objects have runnable examples...
Error in if (line == "## No test: " || insideDontTest || line == "## End(No test)") { :
  missing value where TRUE/FALSE needed
Calls: <Anonymous> ... checkExportsAreDocumented -> doesManPageHaveRunnableExample -> removeDontTest
Execution halted


Regards,

Tiphaine



----------------------------
Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.martin at kcl.ac.uk
Fax: +44 (0) 207 188 6761
Dan Tenenbaum
# 
----- Original Message -----
I don't know what you mean by this, but maybe I should.
If the function is exported, it must have a runnable example.
Can you file an issue at https://github.com/Bioconductor/BiocCheck/issues and include the name of the package?
I will get to it as soon as I can.

Dan
Michael Lawrence
# 
It would be nice to know the use case of the internal keyword here. I've
use it to avoid listing functions in the index (RGtk2 has thousands of
functions). But in general, it's not a good idea to be exporting things
that are truly internal. Perhaps internal methods on exported generics, but
even then, it's probably best to keep the aliases with the generic, or
something.
On Mon, Oct 13, 2014 at 1:33 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Martin, Tiphaine
    

    

      
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Hi,


I wrote a list of functions used in my package called coMET. I decided with my colleagues to try to publish it in Bioconductor. Currently, it has not been yet submitted to bioconductor because I would like to be sure that it satisfies all your guidelines.
A list of functions is useful only internally. I saw that there are two methods to remove the function from the package index and to disable some of their automated tests: the first method is to put a dot as first letter, the second method is to put the "internal" keyword (http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).
I decided to use the second method to reduce to rewrite now all my package.


When I run the new version of BiocCheck Version 1.1.18 with empty \value and \example sections for function with "internal" keyword , I have error message asking to add no-empty runnable examples.

When I run the new version of BiocCheck Version 1.1.18 without \value and \example sections for function with "internal" keyword , I have error message asking to add non-empty \value sections.

with BiocCheck, version 1.0.2, I had a message for functions with "internal" keyword such as "
Checking exported objects have runnable examples...
* CONSIDER: Adding runnable examples to the following man pages
which document exported objects:"

I would like to know if I made a mistake to use internal keyword for this type of functions. What do I need to do ?

Which sections are mandatory in manual file and for which function I need to do a manual file ?


Regards,
Tiphaine

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Hi Tiphaine,

        
On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:

            

      
      
      
    

        
That link is to the documentation of the roxygen2 package. Are you
using roxygen2 to develop your package? You didn't say so.
You say that "you saw that prefixing the function name with a dot
or putting the 'internal' keyword in the man page will 'remove the
function from the package index and disable some of its automated
tests'". I guess that's something you saw in the roxygen2 documentation
right? I don't use roxygene2 myself so I don't know what's the roxygen2
way to control what's exposed or not to the user. However I know many
BioC developers use it for their package so maybe they'll be able to
provide some good advice here.

Keep in mind that using a tool like roxygen2 adds an extra layer of
convenience when developing your package but, unfortunately, it doesn't
completely exempt you from learning and understanding some basic
concepts like NAMESPACE, man pages aliases, keywords, etc...
The ultimate reference for these things is still the "Writing R
Extensions" manual:

   http://cran.r-project.org/doc/manuals/r-release/R-exts.html

So, and FWIW, below I'll describe quickly how you need to proceed when
you don't use a fancy tool like roxygen2 to automatically generate
the NAMESPACE and man pages in your package:

1) The real true way to not expose a function to the user is to not
    export it. What one exports from a package is controlled via
    the NAMESPACE file. So first you need to learn about how to use
    the NAMESPACE file to control exactly what you want to expose to
    the user. See "Writing R Extensions" manual for the details.

2) Every symbol that is exported needs to be documented, that is, there
    must be a man page with an alias for this symbol. And of course
    opening the man page at the R prompt with ?<symbol> should display
    useful information about that symbol.
    'R CMD check' is the tool that will check that every exported
    symbol is documented. It will also perform many checks on the
    man pages to make sure that they are formatted properly.

3) As Dan said previously, any function that is exported also needs
    to have runnable examples and a \value section in its man page.
    Note that this is a Bioconductor requirement, 'R CMD check'
    doesn't check that. 'R CMD BiocCheck' is the tool that will
    perform this check and any other Bioconductor specific check.

            

      
      
      
    

        
Note that, for "plain package development" (i.e. without using a
a fancy tool like roxygen2), using the "internal" keyword in a man
page has no effect on whether the function is exported or not.

            

      
      
      
    

        
These changes in the output of BiocCheck are due to changes in
BiocCheck itself. In particular, the check on \value section was
added recently, and the check on the runnable examples was changed
recently from RECOMMENDED to REQUIRED.

            

      
      
      
    

        
Mandatory sections:

   \name{}
   \alias{}  # you can have more than 1 alias
   \title{}
   \description{}
   \usage{}
   \arguments{}
   \value{}
   \examples{}

Highly recommended sections:

   \seealso{}
   \details{}

            

      
      
      
    

        
Any function that is exported.

Hope this helps,
H.

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Martin, Tiphaine
    

    

      
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Hi Herve,

Thank you for your email. very useful.
But I updated my NAMESPACE in order to list only functions that I want to export.
Even if I did that and if in addition, I keep different man files for functions that I do not want to export, I have this error message.
But if I removed them, I don't have error messages.
I kept different man files for functions that I do not want to export to help my colleagues. It seems that currently, it is not recommended in Bioconductor.

thank you for your help,

Tiphaine

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Hi Tiphaine,

        
On 10/15/2014 06:30 AM, Martin, Tiphaine wrote:

            

      
      
      
    

        
By "colleagues" I guess you mean "co-developers", not "users" of
your package right?

Yes it seems reasonable to expect 'R CMD BiocCheck' to only check
\value and \example for man pages that document exported things.
We should fix that.

Note that it's questionable whether it's a good idea or not to keep
around man pages for non exported things. IMO it's better to document
internal helpers using in-source comments. And since you already
have those in-source comments in place anyway (because you're
using roxygen2), all you need to do is find a way to block
roxygen2 from generating the man pages for these internal helpers.
Co-developers of your package will still be able to see useful
information and that information will be placed where developers
expect it to be: in the source code itself.

My 2 cents.

Cheers,
H.

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin, Tiphaine
    

    

      
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Yep you guess well about my colleagues :) sorry.

Thank you for your advices.
Tiphaine

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
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----- Original Message -----

            

      
      
      
    

        
I am looking at the build report for your latest upload:

http://bioconductor.org/spb_reports/coMET_0.99.2_buildreport_20141016031739.html#oaxaca_check_anchor

I do not see that BiocCheck is complaining about this. 

Are you running BiocCheck on your own machine against a newer version of the package? If so, can you send me the package (off-list)?

If BiocCheck really is doing the wrong thing, I need to be able to reproduce the problem in order to fix it. So I would appreciate it if you can send me a package that causes this problem.

Thanks,
Dan

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Leonardo Collado Torres
    

    

      
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On Thu, Oct 16, 2014 at 7:42 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

            

      
      
      
    

        
Just use a dot at the beginning of the name for your internal
function. Then `devtools` will ignore them. For example, using so with
my package skips the 5 internal functions that have roxygen2 in-source
documentation but that are not exported.

            

      
      
      
    

        
Updating derfinder documentation
Loading derfinder
Skipping invalid path:  .getSegmentsRle.Rd
Skipping invalid path:  .clusterMakerRle.Rd
Skipping invalid path:  .advanced_argument.Rd
Skipping invalid path:  .define_cluster.Rd
Skipping invalid path:  .runFunFormal.Rd

            

      
      
      
    

        
[1] ?1.6.1?

            

      
      
      
    

        
[1] ?4.0.2?

Cheers,
Leo