[Bioc-devel] S4 Methods Documentation Convention Triggers Warnings
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
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