[Bioc-devel] \donttest and the "80% of man pages documenting exported objects must have runnable examples" rule

[Martin Morgan]

On 05/15/2016 02:20 PM, Dan Tenenbaum wrote:
>
>
> ----- Original Message -----
>> From: "Richard Cotton" <richierocks at gmail.com> To: "bioc-devel"
>> <bioc-devel at r-project.org> Sent: Sunday, May 15, 2016 4:45:09 AM
>> Subject: [Bioc-devel] \donttest and the "80% of man pages
>> documenting exported objects must have runnable examples" rule
>
>> I have a package with a lot of examples in exported functions
>> marked as \donttest.
>>
>> BiocCheck doesn't count these functions towards the target of
>> having 80% of exported objects with runnable examples.  I do have
>> more than 80% runnable examples; it's just that BiocCheck can't see
>> them.  (For background, the package is mostly about file import,
>> and it takes a second or two to import the sample files included in
>> the package. Having examples that run for a couple of seconds is
>> fine for users, but makes package testing very slow (once dozens of
>> the example are run).
>>
>> This check is considered REQUIRED to be solved, so I'd like to know
>> if it's OK to include an explanation about the use of \donttest
>> during submission, or if my pacakge will just get rejected
>> outright.
>>
>
>
> Ultimately, humans make all decisions about package inclusion. So you
> will have a chance to discuss your package with someone.

Examples traditionally have dual roles in illustrating functionality and 
testing code. It would be particularly favorable if you could point to 
other parts of your package where the code was tested -- unit tests via 
RUnit or testthat being a natural place, see 
http://bioconductor.org/developers/how-to/unitTesting-guidelines/ -- and 
it's use illustrated -- vignettes or other examples.

Martin

>
> DAn
>
>
>> -- Regards, Richie
>>
>> Learning R 4dpiecharts.com
>>
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