Linking to the manual _file_ is now enforced on CRAN. Here is how to get the file name:
> help("clone.ff", package = "ff")[[1]] [1] "/Users/gaborcsardi/Library/R/4.0/library/ff/help/clone" So in this case you need to link to 'clone'. Btw. since you already use roxygen2, you could also turn on markdown support, and then [ff::clone.ff()] automatically creates the right links in the latest version of roxygen2. Gabor On Wed, Jul 1, 2020 at 6:46 PM Dr. Jens Oehlschlägel <jens.oehlschlae...@truecluster.com> wrote: > > 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