[R-pkg-devel] check cross-references error: Non-file package-anchored link(s)
Gábor Csárdi
c@@rd|@g@bor @end|ng |rom gm@||@com
Thu Jul 2 11:20:00 CEST 2020
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.gorecki using 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, <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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>> >
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>>
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