On 10/25/2013 11:26 AM, Michael Lawrence wrote:
On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen <
kasperdanielhan...@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.
Cheers,
H.
Michael
Comments?
Best,
Kasper
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpa...@fhcrc.org
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