[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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