> ... you could set \RdOpts{stage=build} before the Rd section containing that
> "scary"
\doi (and if needed revert to \RdOpts{stage=install} afterwards).
This works but R-devel CMD check then gives the warning that "Found the
following URL's which should use doi ...".
For a reprex, see the package at
https://github.com/GeoBosh/reprexes/tree/master/redundantDots (man/fun_3.Rd
contains the \doi's).
Building that package with R-devel throws one warning, building it with
non-R-devel throws two (my R-devel is from yesterday, r81914). The latter seems
logical since with older R's \doi is expanded and therefore contains the
expanded URL about which R-devel complains. The warnings do seem somewhat
unpredictable in that I tried different examples and sometimes got warnings
sometimes didn't.
I may be missing something but would it be reasonable not to apply this check
to packages submitted to CRAN until this is made stable?
Georgi Boshnakov
--
Message: 4
Date: Wed, 16 Mar 2022 01:07:54 +0100
From: Sebastian Meyer
To: Ivan Krylov
Cc:
Subject: Re: [Rd] stage=install in \doi definition could lead to
problems
Message-ID: <3ca49400-0f53-708b-72b2-017d2f173...@fau.de>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Am 15.03.22 um 21:38 schrieb Ivan Krylov:
> Good Sys.time() everyone,
>
> If this is not the right place for such questions, please let me know.
Thank you for your feedback! I think this is the right place (but note
that such very recent changes *could* still be work in progress and may
sometimes need a bit more time to be worth discussing here).
>
> I was wondering why \doi has been changed to stage=install instead of
> stage=build in r81891 [1]. I think it might lead to problems, but in
> the spirit of Chesterton's fence, I'd like to learn the reasons. Is it
> to make R CMD build more performant, avoiding the need for the
> "installing the package to process man pages" step for the common case
> of the \doi macro?
Yes, that certainly is one of the advantages of the change, affecting
more than 1000 packages on CRAN that currently ship a partial Rd db just
because they use the \doi macro. Besides considerably speeding up R CMD
build for these packages, the change also slightly reduces the size of
the tarballs.
I think the most probable reason for the previous use of stage=build for
that Sexpr was to avoid shipping the PDF package manual with the
package, as generally triggered by install or render time Sexprs. This
has now been addressed.
>
> Some DOIs look a bit scary. One example that comes to mind is as
> follows:
>
> 10.1002/(SICI)1099-128X(199801/02)12:1<55::AID-CEM501>3.0.CO;2-#
>
> Until the recent fix in r81817 [2], it used to require special
> treatment in order to display correctly in a man page, but now it just
> works if I copy and paste it into \doi{}. With the macro definition
> using [stage=build], I could build a package with a recent build of
> R-devel, get the correct \doi expansion inlined, install the package on
> an older version of R, and it would still work, thanks to R keeping the
> parse tree in build/partial.rdb.
>
> With the macro defined using [stage=install], any version of R older
> than 2022-02-25 (r81817), which doesn't have this fix, would fail to
> link to the DOI correctly, not having the correct expansion of \doi
> to rely upon any more:
>
> Rd2HTML(parse_Rd(textConnection('\\name{foo}\n\\title{bar}\\description{\\doi{10.1002/(SICI)1099-128X(199801/02)12:1<55::AID-CEM501>3.0.CO;2-#}}'),
> fragment = FALSE), stages = c('build'))
>
> href="http://doi.org/10.1002/(SICI)1099-128X(199801/02)12:1%3C55::AID-CEM501%3E3.0.CO;2-#">doi:
> 10.1002/(SICI)1099-128X(199801/02)12:1<55::AID-CEM501>3.0.CO;2-#
>
> (The hash sign doesn't get URL-encoded, and the link gets broken.)
>
> Sorry for giving you yet another case of . If I
> have to, I might be able to "unroll" the macro myself for the few cases
> where it matters.
>
Thank you for the example. I think there is another solution: you could
set \RdOpts{stage=build} before the Rd section containing that "scary"
\doi (and if needed revert to \RdOpts{stage=install} afterwards). Then
the corresponding Sexpr would get evaluated during the build stage as
before and the correctly escaped hyperlink from building with
R-devel/4.2.0 would be available also in older R versions.
Sebastian
--
Message: 5
Date: Wed, 16 Mar 2022 13:14:32 +0300
From: Ivan Krylov
To: Sebastian Meyer
Cc:
Subject: Re: [Rd] stage=install in \doi definition could lead to
problems
Message-ID: <20220316131432.5fe64185@arachnoid>
Content-Type: text/plain; charset="us-ascii"
On Wed, 16 Mar 2022 01:07:54 +0100
Sebastian Meyer wrote:
> I think there is another solution: you could set \RdOpts{stage=build}
> before the Rd section containing that "scary" \doi (and if needed
> revert to \RdOpts{stag
