[Bioc-devel] runnable examples for internal function ?

[Martin, Tiphaine]

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


________________________________
From: Michael Lawrence <lawrence.michael at gene.com>
Sent: 13 October 2014 21:52
To: Dan Tenenbaum
Cc: Martin, Tiphaine; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] runnable examples for internal function ?

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<mailto:dtenenba at fhcrc.org>> wrote:


----- Original Message -----
> From: "Tiphaine Martin" <tiphaine.martin at kcl.ac.uk<mailto:tiphaine.martin at kcl.ac.uk>>
> To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
> Sent: Monday, October 13, 2014 1:29:08 PM
> Subject: [Bioc-devel] runnable examples for internal function ?
>
> 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 don't know what you mean by this, but maybe I should.

>
> 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:"
>

If the function is exported, it must have a runnable example.


> 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
>

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


>
> 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<mailto:tiphaine.martin at kcl.ac.uk>
> Fax: +44 (0) 207 188 6761<tel:%2B44%20%280%29%20207%20188%206761>
>
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>
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