Thank you Gabor
On Thu, Jul 2, 2020 at 10:20 AM Gábor Csárdi <csardi.ga...@gmail.com> wrote:
>
> You can set the _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true env var and
> use R-devel.
>
> Alternatively, and you don't need R-devel for this, you can run R CMD
> --html INSTALL on your package, and then look for messages that
> contain "treated as a topic", e.g.
>
> curl_fds html
> Rd warning: /Users/gaborcsardi/works/processx/man/curl_fds.Rd:11: file
> link ‘multi_fdset’ in package ‘curl’ does not exist and so has been
> treated as a topic
>
> Gabor
>
>
> On Thu, Jul 2, 2020 at 10:06 AM Jan Gorecki <j.gore...@wit.edu.pl> wrote:
> >
> > Hi,
> > What is the recommended way to test for those issues locally?
> > If it is tested during cran submission, then seems reasonable to be enabled
> > just by --as-cran switch. Is it?
> > Thanks
> >
> > On Wed 17 Jun, 2020, 12:32 AM Wayne Oldford, <rwoldf...@uwaterloo.ca> wrote:
> >>
> >> Thank you!
> >>
> >> -----Original Message-----
> >> From: Gábor Csárdi <csardi.ga...@gmail.com>
> >> Date: Tuesday, June 16, 2020 at 4:32 PM
> >> To: Wayne Oldford <rwoldf...@uwaterloo.ca>
> >> Cc: List r-package-devel <r-package-devel@r-project.org>
> >> Subject: Re: [R-pkg-devel] check cross-references error: Non-file
> >> package-anchored link(s)
> >>
> >> This is how to look up the filename. The first "sp" is the topic name,
> >> the second is the package name.
> >>
> >> > help("sp", "sp")[[1]]
> >> [1] "C:/Users/csard/R/win-library/4.0/sp/help/00sp"
> >>
> >> So you need to link to the "00sp.Rd" file: \link[sp:00sp]{sp}
> >>
> >> Gabor
> >>
> >> On Tue, Jun 16, 2020 at 9:09 PM Wayne Oldford <rwoldf...@uwaterloo.ca>
> >> wrote:
> >> >
> >> > Hi
> >> >
> >> > I got caught by this new test this week in trying to push an updated
> >> release of the loon package to CRAN.
> >> >
> >> > By following this thread, I corrected my cross-references to
> >> external packages but I got stymied by
> >> > the one I hoped to give to the "sp" package for Spatial data
> >> >
> >> > _________
> >> >
> >> > Here is the history:
> >> >
> >> > I tried
> >> > \link[sp:sp]{sp}
> >> > which failed here:
> >> > Debian:
> >> <https://win-builder.r-project.org/incoming_pretest/loon_1.3.1_20200616_162128/Debian/00check.log>
> >> > Status: 1 WARNING
> >> >
> >> >
> >> > That was meant to correct an earlier attempt (it did for other links
> >> to "scales" for example) where I had tried
> >> > \link[sp]{sp}
> >> > and failed here:
> >> > Debian:
> >> <https://win-builder.r-project.org/incoming_pretest/loon_1.3.1_20200615_213749/Debian/00check.log>
> >> > Status: 1 WARNING
> >> >
> >> >
> >> > So to complete the possibilities as I understand them, I just now
> >> tried
> >> > \link{sp}
> >> > which, as might be expected, failed here:
> >> > Debian:
> >> <https://win-builder.r-project.org/incoming_pretest/loon_1.3.1_20200616_213921/Debian/00check.log>
> >> > Status: 1 WARNING
> >> > As expected, error here was different: "Missing link" as opposed
> >> to "Non-file package-anchored link"
> >> >
> >> > _________
> >> >
> >> >
> >> > I am not sure whether I have missed a subtlety in WRE or that the
> >> peculiar circumstance
> >> > where the package, the topic, and the file name are all identical
> >> (sp) is some weird boundary case.
> >> >
> >> > Without further advice, I think I am just going to remove the link
> >> to "sp".
> >> > It really is just a courtesy link to the package description for
> >> "sp".
> >> >
> >> > Thanks in advance for your thoughts.
> >> >
> >> > Wayne
> >> >
> >> >
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: R-package-devel <r-package-devel-boun...@r-project.org> on
> >> behalf of Georgi Boshnakov <georgi.boshna...@manchester.ac.uk>
> >> > Date: Tuesday, June 16, 2020 at 9:27 AM
> >> > To: Gábor Csárdi <csardi.ga...@gmail.com>, Duncan Murdoch
> >> <murdoch.dun...@gmail.com>
> >> > Cc: List r-package-devel <r-package-devel@r-project.org>
> >> > Subject: Re: [R-pkg-devel] check cross-references error: Non-file
> >> package-anchored link(s)
> >> >
> >> > I think that the current behaviour is documented in WRE:
> >> >
> >> > "...There are two other forms of optional argument specified as
> >> \link[pkg]{foo} and
> >> > \link[pkg:bar]{foo} to link to the package pkg, to files
> >> foo.html and bar.html respectively.
> >> > These are rarely needed, perhaps to refer to not-yet-installed
> >> packages (but there the HTML
> >> > help system will resolve the link at run time) or in the
> >> normally undesirable event that more
> >> > than one package offers help on a topic7 (in which case the
> >> present package has precedence so
> >> > this is only needed to refer to other packages). They are
> >> currently only used in HTML help
> >> > (and ignored for hyperlinks in LATEX conversions of help pages),
> >> and link to the file rather
> >> > than the topic (since there is no way to know which topics are
> >> in which files in an uninstalled
> >> > package) ... Because they have been frequently misused, the
> >> HTML help system looks for topic foo in package pkg
> >> > if it does not find file foo.html."
> >> >
> >> > Unless I am missing something, it seems that it would be
> >> relatively painless to reverse the logic of the current behaviour of the
> >> help system,
> >> > i.e. to start looking first for the topic and then for a file.
> >> >
> >> > Georgi Boshnakov
> >> >
> >> > -----Original Message-----
> >> > From: R-package-devel <r-package-devel-boun...@r-project.org> On
> >> Behalf Of Gábor Csárdi
> >> > Sent: 16 June 2020 13:44
> >> > To: Duncan Murdoch <murdoch.dun...@gmail.com>
> >> > Cc: List r-package-devel <r-package-devel@r-project.org>
> >> > Subject: Re: [R-pkg-devel] check cross-references error:
> >> Non-file package-anchored link(s)
> >> >
> >> > On Mon, Jun 15, 2020 at 5:30 PM Duncan Murdoch
> >> <murdoch.dun...@gmail.com> wrote:
> >> > >
> >> > > On 15/06/2020 12:05 p.m., Martin Maechler wrote:
> >> > > >>>>>> Duncan Murdoch on Sun, 14 Jun 2020 07:28:03 -0400
> >> writes:
> >> > > >
> >> > > > > I agree with almost everything you wrote, except one
> >> thing: this isn't
> >> > > > > newly enforced, it has been enforced since the help
> >> system began. What
> >> > > > > I think is new is that there are now tests for it.
> >> Previously those
> >> > > > > links just wouldn't work.
> >> > > >
> >> > > > > Duncan Murdoch
> >> > > >
> >> > > > Yes, to all... including Duncan's agreement with Gábor.
> >> > > >
> >> > > > Also, Duncan M earlier did mention that he had wanted to
> >> > > > *change* the link-to-file behavior for these cases (when he
> >> wrote
> >> > > > most of the Rd2html source code) but somehow did not get it.
> >> > >
> >> > > Actually, I don't think I pushed for this change at the time
> >> (or at
> >> > > least I didn't push much). I just wish now that I had,
> >> because I
> >> > > think it will be harder to do it now than it would have been
> >> then.
> >> > >
> >> > > Duncan
> >> >
> >> > I am not entirely sure, but maybe just documenting the current
> >> behaviour and undoing 78674 could work. With some tweaks? E.g.
> >> >
> >> > * updating R-exts to say that \link[pkg:topic]{text} will link
> >> to `topic.html` in `pkg` first (for historical reasons), and falls back to
> >> searching for `topic` in `pkg` at render time.
> >> > * updating Rd2HTML to look for the topic and use it in the link,
> >> instead of throwing a warning, in it cannot find `topic.html`
> >> > * removing the `R CMD check` warning for non-file links, that
> >> was added in 78674 :)
> >> >
> >> > Is there anything else?
> >> >
> >> > Gabor
> >> >
> >> > [...]
> >> >
> >> > ______________________________________________
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> >> > ______________________________________________
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> >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> >
> >> >
> >> > ______________________________________________
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> >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >>
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