[Bioc-devel] role of replaceSlots in BiocGenerics

[Hervé Pagès]

One of the reasons it's not exported is because it started as something
kind of experimental and we didn't find a good home for it yet. I could
probably move it to S4Vectors where we already have some low-level
S4-related utils. Not the best home either but maybe better than in
BiocGenerics?

IMO using something like replaceSlots() or initialize() is still better
than using direct slot assignment when you need to replace more than 1
slot. It's more compact and provide an all-slots-are-modified-at-once
semantic (atomicity) which can be useful if modifying the slots one
after the other could temporarily create an invalid object.

H.

On 09/06/2017 03:41 PM, Vincent Carey wrote:
> I am getting complaints from CMD check about ::: which seems necessary to
> use this replaceSlots facility because it is not exported.  I will look
> into initialize,
> which might work fine for my concern.  I cannot remember why I did not just
> use direct assignment to slots, however.  Perhaps I just found the
> function and
> decided using it would be better.  It would be nice to export replaceSlots
> if it does not contravene an important principle.
>
> On Wed, Sep 6, 2017 at 5:23 PM, Hervé Pagès <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
>     Hi,
>
>     Personally I like replaceSlots() better.
>
>     Not only because it's more readable but also the fact that you can use
>     initialize() to update an existing object is an undocumented feature so
>     I prefer to not rely on it.
>
>     Also initialize() is a generic and there could be a method defined for
>     the object you're trying to update that won't behave the way you expect
>     (e.g. the names of its arguments won't necessarily match the names of
>     the slots).
>
>     Also validation can be expensive and there are many situations where
>     you know that you're replacing the object slots with thiings that
>     don't break the object so I like that I can call replaceSlots() with
>     check=FALSE.
>
>     I actually wish the methods package had something like replaceSlots().
>
>     H.
>
>     On 09/06/2017 01:11 PM, Michael Lawrence wrote:
>
>         No, the best practice is to just use initialize(). It used to be
>         that
>         replaceSlots() saved some copying, but that's no longer really the
>         case. The only potential benefit is that it can skip validity
>         checks,
>         but usually you want those.
>
>         Michael
>
>         On Wed, Sep 6, 2017 at 12:55 PM, Vincent Carey
>         <stvjc at channing.harvard.edu <mailto:stvjc at channing.harvard.edu>>
>         wrote:
>
>             Is this the preferred way of adjusting content in a
>             live object?  It is not accessible except via ":::"
>
>                       [[alternative HTML version deleted]]
>
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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
>     Seattle, WA 98109-1024
>
>     E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>

-- 
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
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319