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-boun...@r-project.org> Im Auftrag von Martin
> Morgan
> Gesendet: Donnerstag, 13. Februar 2020 04:46
> An: stefano <mangiolastef...@gmail.com>; bioc-devel@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-boun...@r-project.org on behalf of mangiolastef...@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]]
>
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