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
