[R-pkg-devel] check cross-references error: Non-file package-anchored link(s)
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Thu Jul 2 13:26:02 CEST 2020
There are a few ways to deal with this, but waiting for ff to be updated
is probably easiest.
However, maybe ff can't be updated until bit is updated. Here are some
possibilities:
One way is to make bit depend on a particular version of ff. That may
cause a deadlock if both are being updated at once, but I think CRAN
should be able to deal with it if they are informed of the issue.
Another way is to use R code in the Rd file to select which link to use.
For example, instead of \link[ff]{clone.ff}, you could use
\Sexpr[results=rd,stage=render]{clonelink()}
where clonelink() is a function that generates either
"\link[ff]{clone.ff}" or "\link[ff:clone]{clone.ff}" depending on the
detected installed version of ff.
Another choice that is nearly as easy as doing nothing is to include no
link at all in this update, and make it a link again in the next update
when the new ff is available.
Duncan Murdoch
On 02/07/2020 6:47 a.m., Dr. Jens Oehlschlägel wrote:
> Thanks Gabor and Duncan,
>
>> It's actually in ff/man/clone.rd, not clone.ff.rd. There is no
>> ff/man/clone.ff.rd file.
>
> but there *is* clone.ff.rd in the >= 4.0.0 versions of the packages bit/bit64/ff.
>
> Hence the check warning is a false alarm resulting from checking bit 4.0.2 (GitHub.com/truecluster) against ff 2.2-14.2 (CRAN) instead of checking it against the also submitted ff 4.0.2 (GitHub.com/truecluster).
>
> So all I can and will do is waiting that CRAN maintainers install and check again.
>
> Best
>
> Jens
>
>
>
>>
>> Duncan Murdoch
>>
>>>
>>> Best regards
>>>
>>> Jens
>>>
>>>
>>>
>>>
>>> On 16.06.20 22:31, Gábor Csárdi wrote:
>>>> 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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