[Bioc-devel] EXTERNAL: Not possible to create runnable examples for package

Marcel Ramos m@rce|@r@mo@perez @end|ng |rom ro@we||p@rk@org
Tue Aug 10 21:27:51 CEST 2021

Hi Kelsey,

One of the main reasons we have that 80% check is to induce modularity 
in a package.
You can chain examples from several R files / functions in sequence 
according to
collation order (collation field in the DESCRIPTION or alphabetical order).

Ideally, you can use a small dataset for the examples and demonstrate 
the use
of the functions in your package. In the end, these examples will be very
useful for your users.

We do make rare exceptions to this rule mainly for non code based packages
e.g., ExperimentHub.

One could argue that if the functions are very complicated or difficult,
it may not be a package that users will find easy to use and that
some redesign would be apt.

Best regards,


On 8/10/21 11:48 AM, Kelsey Chetnik via Bioc-devel wrote:
> I am preparing a package for submission to Bioconductor. One of the errors I got from running BioCheck() was "At least 80%of man pages documenting exported objects must have runnable examples". The way our package is constructed makes meeting this requirement practically impossible.
> Our package is designed to create pipelines by chaining functions and saving intermediate results in an object. These functions are not meant to be run in small examples - many require a series of other functions to be run before they can be called. It wouldn't be possible to make the examples runnable without either large intermediate objects that would cause our package to exceed the size limit of 5 MB or long examples that could consist of 20+ lines of code. It would also be very complicated and difficult to maintain these examples.
> Is it possible for our package to be accepted without resolving this issue if we provide justification for it?
> Thank you,
> Kelsey
> 	[[alternative HTML version deleted]]
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Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263

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