[Rd] advise on Depends

Hervé Pagès hpages at fhcrc.org
Sat Oct 26 03:05:51 CEST 2013

On 10/25/2013 11:26 AM, Michael Lawrence wrote:
> On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>> This is about the new note
>> Depends: includes the non-default packages:
>>    ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’
>>    ‘Biostrings’ ‘bumphunter’
>> Adding so many packages to the search path is excessive and importing
>> selectively is preferable.
>> Let us say my package A either uses a class B (by producing an object that
>> has B embedded as a slot) from another package or provides a specific
>> method for a generic defined in another package (both examples using S4).
>>   In both case my impression is that best practices is I ought to Depend on
>> such a package, so it is a available at run time to the user.
> For classes, you just need to import the class with importClassesFrom().
> For generics, as long as your package exports the method with
> exportMethods(), the generic will also be exported from your package,
> regardless of whether the defining package is attached. And the methods
> from the loaded-but-not-attached packages are available for the generic. So
> neither of these two is really a problem.
> The rationale for Depends is that the user might always want to use
> functions defined by another package with objects consumed/produced by your
> package, such as generics for which your package has not defined any
> methods. For example, rtracklayer Depends on GenomicRanges, because it
> imports objects from files as GenomicRanges objects.  So just consider what
> the user sees when looking at your API. What's private, what's public?

And also the user should be able to use ? to access the full
documentation of what is public. This means that if your package
defines and exports a method for a generic defined elsewhere, it should
"Depends" on the package where the generic is defined. Same thing if
your package extends a class defined elsewhere.


> Michael
>> Comments?
>> Best,
>> Kasper
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Hervé Pagès

Program in Computational Biology
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