[Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2>

[Håkon Tjeldnes]

Two ways works for me, either link to the Rd file or only use tokens.


Don't know what is best, but I use tokens, that is :


\code{\link[MSnbase:pickpeaks-method]{pickPeaks}} ----becomes---> \code{\link{pickPeaks}}


On Windows, when you install, it will automatically find the correct links.


Someone from BioC should confirm that what I am saying is correct and a safe way of doing it.

________________________________
Fra: Bioc-devel <bioc-devel-bounces at r-project.org> p� vegne av Mike Smith <grimbough at gmail.com>
Sendt: 16. april 2018 12:13
Til: Rainer Johannes; bioc-devel

 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.Rainer at 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

he

> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith <grimbough at 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.Rainer at 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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