And I have now asked this in R-pkg-devel (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as suggested by Martin Maechler (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the thread linked by Lori.
But if you can use \link{foo} (instead of \link[pkg]{foo} and \link[pkg:bar]{foo}), as also suggested by Håkon Tjeldnes, then you should have no problems. Best, R. On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > This was also discussed in this thread a few weeks ago > > https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Mike Smith > <grimbo...@gmail.com> > Sent: Monday, April 16, 2018 6:13:38 AM > To: Rainer Johannes; bioc-devel > Subject: Re: [Bioc-devel] Windows <Problems with Rd links to other packages > on Tokay2> > > Martin mentioned that he changed the wording in > https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e > , so more recently than your version of R-devel. > > Mike > > On 16 April 2018 at 11:57, Rainer Johannes <johannes.rai...@eurac.edu> > wrote: > >> Thanks Mike, >> >> I somehow missed the discussion you mentioned. I would really not like to >> include the name of the Rd file I want to link to. The *default* way that >> works on Linux and macOS should also work on Windows - otherwise what's the >> matter of the alias? Interestingly, on my Windows test machine (Windows 7) >> I don't get these warnings (R-devel from 2018-01-07 r74091). >> >> jo >> >> > On 16 Apr 2018, at 10:49, Mike Smith <grimbo...@gmail.com> wrote: >> > >> > Hi Johannes, >> > >> > xcms is certainly not alone with the warning, and it was discussed in >> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html >> > >> > I think you should be able to get round it by including the name of Rd >> file you're linking to e.g. >> \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} >> (I haven't actually tested this though). >> > >> > Mike >> > >> > On 16 April 2018 at 09:06, Rainer Johannes <johannes.rai...@eurac.edu> >> wrote: >> > Dear all, >> > >> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to >> links in Rd files to functions and methods in other packages. >> > Example: >> > we have \code{\link[MSnbase]{pickPeaks}} in >> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that >> works nicely on Linux and macOS build machines, but on tokay2 we get: >> > >> > Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R. >> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link >> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as >> a topic >> > >> > is there any other solution to removing all links to external packages? >> > >> > thanks, jo >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel