[R-pkg-devel] check cross-references error: Non-file package-anchored link(s)
Dr. Jens Oehlschlägel
jen@@oeh|@ch|@ege| @end|ng |rom truec|u@ter@com
Wed Jul 1 19:46:13 CEST 2020
Good evening,
My package bit 4.0.2 (https://github.com/truecluster/bit) is being
rejected by CRAN checks with warning:
>Check: Rd cross-references, Result: WARNING
> Non-file package-anchored link(s) in documentation object 'clone.Rd':
> '[ff]{clone.ff}'
>
> See section 'Cross-references' in the 'Writing R Extensions' manual.
although clone.ff is in clone.ff.rd as confirmed by
> help("clone.ff","ff")[[1]]
[1] "/home/mypc/R/x86_64-pc-linux-gnu-library/4.0/ff/help/clone.ff"
I asked the maintainers to explain what is wrong and what to do and got
no answer. Does someone here can help?
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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