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

[stefano]

Thanks a lot to both.

I have been suggested to try

`usethis::use_pipe(export = TRUE)`

probably put in place because the task is indeed challenging.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno gio 13 feb 2020 alle ore 18:29 Felix Ernst <
felix.gm.ernst using outlook.com> ha scritto:

> 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
>
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>
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