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 <rwoldf...@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-boun...@r-project.org> on behalf of >> Georgi Boshnakov <georgi.boshna...@manchester.ac.uk> >> Date: Tuesday, June 16, 2020 at 9:27 AM >> To: Gábor Csárdi <csardi.ga...@gmail.com>, Duncan Murdoch >> <murdoch.dun...@gmail.com> >> Cc: List r-package-devel <r-package-devel@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-boun...@r-project.org> On Behalf >> Of Gábor Csárdi >> Sent: 16 June 2020 13:44 >> To: Duncan Murdoch <murdoch.dun...@gmail.com> >> Cc: List r-package-devel <r-package-devel@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.dun...@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 >> >> [...] >> >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> >> >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel