[R-pkg-devel] check cross-references error: Non-file package-anchored link(s)
Jan Gorecki
j@goreck| @end|ng |rom w|t@edu@p|
Thu Jul 2 11:04:17 CEST 2020
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, <rwoldford using uwaterloo.ca> wrote:
> Thank you!
>
> -----Original Message-----
> From: Gábor Csárdi <csardi.gabor using gmail.com>
> Date: Tuesday, June 16, 2020 at 4:32 PM
> To: Wayne Oldford <rwoldford using uwaterloo.ca>
> Cc: List r-package-devel <r-package-devel using 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 <rwoldford using 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-bounces using r-project.org> on
> behalf of Georgi Boshnakov <georgi.boshnakov using manchester.ac.uk>
> > Date: Tuesday, June 16, 2020 at 9:27 AM
> > To: Gábor Csárdi <csardi.gabor using gmail.com>, Duncan Murdoch <
> murdoch.duncan using gmail.com>
> > Cc: List r-package-devel <r-package-devel using 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-bounces using r-project.org>
> On Behalf Of Gábor Csárdi
> > Sent: 16 June 2020 13:44
> > To: Duncan Murdoch <murdoch.duncan using gmail.com>
> > Cc: List r-package-devel <r-package-devel using 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.duncan using 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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