Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2023-04-14 Thread Hervé Pagès
Thanks Deepayan. H. On 30/03/2023 02:32, Deepayan Sarkar wrote: R-devel and R-4-3-branch both now have the option of suppressing these warnings by setting _R_CHECK_RD_ALLOW_EMPTY_ITEM_IN_DESCRIBE_=true But please note this is only intended to be a stop-gap measure, and will likely be removed

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2023-03-30 Thread Deepayan Sarkar
R-devel and R-4-3-branch both now have the option of suppressing these warnings by setting _R_CHECK_RD_ALLOW_EMPTY_ITEM_IN_DESCRIBE_=true But please note this is only intended to be a stop-gap measure, and will likely be removed at some point. Best, -Deepayan On Mon, Jan 30, 2023 at 12:02 PM

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2023-01-29 Thread Hervé Pagès
On 28/01/2023 19:42, Deepayan Sarkar wrote: ... I'm open to suppressing the warning for \describe items (the warning is more important for \arguments). Let me know. Hi Deepayan, suppressing the warning for \describe would kind of make sense. Thanks for the offer. Best, H. -- Hervé Pagès

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2023-01-28 Thread Deepayan Sarkar
On Fri, Jan 27, 2023 at 9:26 PM Hervé Pagès wrote: > > On 27/01/2023 02:00, Dario Strbenac via Bioc-devel wrote: > > > Good day, > > > > So, is the ultimate solution to manually change everything to the format of > > > > \item{\code{show(x)}:}{ > >... > > } ? > > I think I will do this in my

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2023-01-27 Thread Hervé Pagès
On 27/01/2023 02:00, Dario Strbenac via Bioc-devel wrote: Good day, So, is the ultimate solution to manually change everything to the format of \item{\code{show(x)}:}{ ... } ? I think I will do this in my own packages. Still need to make those changes though, just didn't have time to

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2023-01-27 Thread Dario Strbenac via Bioc-devel
Good day, So, is the ultimate solution to manually change everything to the format of \item{\code{show(x)}:}{ ... } ? The warnings persist, so it does not seem as though R will revert to allowing the currently-popular syntax past its check. -- Dario

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-12-01 Thread Henrik Bengtsson
le extra (unnecessary) indentation under the > >> original formatting. > >> > >> I changed the ‘Accessors: Back-end control’ to an itemized list, since > >> there was no description associated with each item. This adds bullets. > >> > >> The commit is at

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-12-01 Thread Hervé Pagès
cParallel...) Martin From: Bioc-devel on behalf of Martin Maechler Date: Wednesday, November 30, 2022 at 6:28 AM To: Michael Lawrence (MICHAFLA) Cc: bioc-devel@r-project.org , Kurt Hornik < kurt.hor...@wu.ac.at> Subject: Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-30 Thread Henrik Bengtsson
> Maechler > Date: Wednesday, November 30, 2022 at 6:28 AM > To: Michael Lawrence (MICHAFLA) > Cc: bioc-devel@r-project.org , Kurt Hornik > > Subject: Re: [Bioc-devel] S4 Methods Documentation Convention Triggers > Warnings > >>>>> Michael Lawrence \(M

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-30 Thread Martin Morgan
: bioc-devel@r-project.org , Kurt Hornik Subject: Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings >>>>> Michael Lawrence \(MICHAFLA\) via Bioc-devel >>>>> on Mon, 28 Nov 2022 12:11:00 -0800 writes: > It may be worth revisiting

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-30 Thread Martin Maechler
> Michael Lawrence \(MICHAFLA\) via Bioc-devel > on Mon, 28 Nov 2022 12:11:00 -0800 writes: > It may be worth revisiting why we arrived at this convention in the first > place and see whether the Rd system can be enhanced somehow so that we can > achieve the same effect

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-28 Thread Michael Lawrence (MICHAFLA) via Bioc-devel
It may be worth revisiting why we arrived at this convention in the first place and see whether the Rd system can be enhanced somehow so that we can achieve the same effect with a more natural syntax. Michael On Mon, Nov 28, 2022 at 11:25 AM Deepayan Sarkar wrote: > On Sun, Nov 27, 2022 at

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-28 Thread Deepayan Sarkar
On Sun, Nov 27, 2022 at 12:30 PM Dario Strbenac via Bioc-devel < bioc-devel@r-project.org> wrote: > Good day, > > For a long time, it has been a convention to document S4 methods in the > format: > > \section{Displaying}{ > In the code snippets below, \code{x} is a GRanges object. >

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-27 Thread Henrik Bengtsson
What about: \item{\code{show(x)}}{ Displays the first five and last five elements. } ? On Sat, Nov 26, 2022, 23:00 Dario Strbenac via Bioc-devel < bioc-devel@r-project.org> wrote: > Good day, > > For a long time, it has been a convention to document S4 methods in the > format: > >

[Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

2022-11-26 Thread Dario Strbenac via Bioc-devel
Good day, For a long time, it has been a convention to document S4 methods in the format: \section{Displaying}{ In the code snippets below, \code{x} is a GRanges object. \describe{ \item{}{ \code{show(x)}: Displays the first five and last five elements. } } } In R