Message-ID: <CAFDcVCSbHXXqC2ib39om1=qmOi021ERbPD7reFKj5v=Kab0srQ@mail.gmail.com>
Date: 2022-11-30T17:36:05Z
From: Henrik Bengtsson
Subject: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings
In-Reply-To: <BY5PR04MB6627C0059DF9EB80FC9E08F3F9159@BY5PR04MB6627.namprd04.prod.outlook.com>
> I think in \item{<foo>}{bar} the <foo> is not wrapped, so runs off the margin in the devel ?Constructor? section.
Would a hack be to split up the \code{} in multiple ones, e.g.
\item{
\code{SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),}
\code{tasks = 0L, stop.on.error = FALSE,}
\code{progressbar = FALSE, RNGseed = NULL,}
\code{timeout = Inf, exportglobals = TRUE,}
\code{exportvariables = TRUE,}
\code{log = FALSE, threshold = "INFO", logdir = NA_character_,}
\code{resultdir = NA_character_, jobname = "BPJOB",}
\code{manager.hostname = NA_character_,}
\code{manager.port = NA_integer_,}
\code{...)}}:}{
Does that line wrap?
/Henrik
On Wed, Nov 30, 2022 at 8:21 AM Martin Morgan <mtmorgan.bioc at gmail.com> wrote:
>
> I recently made the change Henrik suggests in the ?devel? but not ?release? branch of BiocParallel, so the manuals can be compared. Take a look at the ?Constructor? and ?Accessors: Logging and results? sections of the ?SnowParam-class.Rd? man page, starting on p. 53 of the PDF.
>
> https://bioconductor.org/packages/release/bioc/manuals/BiocParallel/man/BiocParallel.pdf
>
> https://bioconductor.org/packages/devel/bioc/manuals/BiocParallel/man/BiocParallel.pdf
>
> I think in \item{<foo>}{bar} the <foo> is not wrapped, so runs off the margin in the devel ?Constructor? section. The shorter items in the ?Accessors: Logging and results? section look almost identical, with a little 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
>
> https://code.bioconductor.org/browse/BiocParallel/commit/4e85b38b92f2adb68fe04ffb0476cbc47c1241a8
>
> (as well as https://github.com/Bioconductor/BiocParallel...)
>
> Martin
>
> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Martin Maechler <maechler at stat.math.ethz.ch>
> Date: Wednesday, November 30, 2022 at 6:28 AM
> To: Michael Lawrence (MICHAFLA) <lawrence.michael at gene.com>
> Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>, Kurt Hornik <Kurt.Hornik at wu.ac.at>
> 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 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
>
>
> Yes, I agree.
>
> It may be that in the distant past, Henrik's suggestion
> (a version of which I am using myself a lot in *.Rd -- mostly
> *not* related to S4)
> did not work correctly, but I know it has worked for years now,
> as I use it "all the time".
> and not just I.
>
> If I grep in R's *base* package alone,
>
> inside ...../R/src/library/base/man/
>
> grep --color -nH --null -e '\\item{\\code{<file:///item%7b/code%7b>' *.Rd
>
> starts with
>
> agrep.Rd
>
> [[alternative HTML version deleted]]
>
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