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 <hpa...@fredhutch.org <mailto:hpa...@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 <st...@channing.harvard.edu <mailto:st...@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]] _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iXa2JnAchBDp8QpTOD4yZHTEXOMu5gjBfDOMcvQCriU&s=0Rbio7Sp7SXzPgU4xGDGkWA7V-tkgkDizVkI9JMYQ2g&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iXa2JnAchBDp8QpTOD4yZHTEXOMu5gjBfDOMcvQCriU&s=0Rbio7Sp7SXzPgU4xGDGkWA7V-tkgkDizVkI9JMYQ2g&e=> _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iXa2JnAchBDp8QpTOD4yZHTEXOMu5gjBfDOMcvQCriU&s=0Rbio7Sp7SXzPgU4xGDGkWA7V-tkgkDizVkI9JMYQ2g&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iXa2JnAchBDp8QpTOD4yZHTEXOMu5gjBfDOMcvQCriU&s=0Rbio7Sp7SXzPgU4xGDGkWA7V-tkgkDizVkI9JMYQ2g&e=> -- 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: hpa...@fredhutch.org <mailto:hpa...@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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
