[Bioc-devel] EXTERNAL: Re: warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic

[stefano]

Thanks a lot I will try.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno ven 14 feb 2020 alle ore 02:49 Marcel Ramos <
Marcel.Ramos using roswellpark.org> ha scritto:

> Hi Stefano,
>
> I'm no roxygen expert either but you could try using the
> `usethis::use_pipe(export = TRUE)`
> functionality developed by actual roxygen experts ;)
>
> Best,
> Marcel
>
> On 2/13/20 2:28 AM, Felix Ernst wrote:
> > Hi,
> >
> > I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to
> implicit for anyone's taste, \code{\link[magrittr:pipe]{\%>\%}} should also
> work in this case.
> >
> > The case above is used for a package external link. For an internal
> explicit link use \code{\link[=something]{or other}}.
> >
> > Felix
> >
> > -----Ursprüngliche Nachricht-----
> > Von: Bioc-devel <bioc-devel-bounces using r-project.org> Im Auftrag von
> Martin Morgan
> > Gesendet: Donnerstag, 13. Februar 2020 04:46
> > An: stefano <mangiolastefano using gmail.com>; bioc-devel using r-project.org
> > Betreff: Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr'
> does not exist and so has been treated as a topic
> >
> > This warning
> >
> > * checking whether package 'ttBulk' can be installed ... WARNING Found
> the following significant warnings:
> >   Rd warning:
> C:/Users/pkgbuild/AppData/Local/Temp/Rtmp6Js8e8/R.INSTALL1ddcdee5581/ttBulk/man/reexports.Rd:19:
> file link '%>%' in package 'magrittr' does not exist and so has been
> treated as a topic See
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1330/8048f88/ttBulk.Rcheck/00install.out'
> for details.
> >
> > is actually about the documentation for '%>%'. In your previous 'man'
> page you had
> >
> >   \code{\link[magrittr]{\%>\%}}
> >
> > which from reading 'Writing R Extensions' RShowDoc("R-exts") section 2.5
> 'Cross-references' indicates that you're trying to link to an html page
> named '%>%.html' in the magrittr package, but actually the man page is
> 'pipe.html' (e.g., by using help.start() and browsing manually to the help
> page). While it's possible to link to that help page, you should instead
> just \code{\link{\%>\%}} and R (possibly with the user choosing the
> package) will generate the correct link.
> >
> > Your package is too deep into the roxygen foo for me to know what you
> need to do to generate the appropriate link (or even where the link is
> generated...); maybe there's a roxygen expert on the mailing list who can
> help (or you can perhaps post here where you generate the reexports.Rd page
> from).
> >
> > Also, your github repository seems VERY LARGE (I lost patience trying to
> clone it, although my current link is quite slow); this
> http://bioconductor.org/developers/how-to/git/remove-large-data/ might
> provide some hints for removing large commits.
> >
> > Hope that helps,
> >
> > Martin
> >
> >
> > On 2/12/20, 9:51 PM, "Bioc-devel on behalf of stefano" <
> bioc-devel-bounces using r-project.org on behalf of mangiolastefano using gmail.com>
> wrote:
> >
> >     Hello Community,
> >
> >     The CHECK Windows server gives me a warning when I try to reexport an
> >     existing operator magrittr::`%>%`
> >
> >     ```
> >     #' @importFrom magrittr %>%
> >
> >     #' @export
> >
> >     magrittr::`%>%`
> >     ```
> >
> >     okay2 Windows Server 2012 R2 Standard/x64
> >       OK
> >       WARNINGS
> >       OK
> >       OK
> >
> >     malbec2 Linux (Ubuntu 18.04.3 LTS)/x86_64
> >       OK
> >       OK
> >       skipped
> >       OK
> >
> >
> >     Here is the log
> >
> http://bioconductor.org/spb_reports/ttBulk_buildreport_20200212081044.html#tokay2_check_anchor
> >
> >     I looked online but I could not find a definitive answer. An advice
> will be
> >     highly appreciated.
> >
> >     Thanks!
> >
> >     Best wishes.
> >
> >     *Stefano *
> >
> >
> >
> >     Stefano Mangiola | Postdoctoral fellow
> >
> >     Papenfuss Laboratory
> >
> >     The Walter Eliza Hall Institute of Medical Research
> >
> >     +61 (0)466452544
> >
> >       [[alternative HTML version deleted]]
> >
> >     _______________________________________________
> >     Bioc-devel using r-project.org mailing list
> >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]