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

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

-----Urspr?ngliche Nachricht-----
Von: Bioc-devel <bioc-devel-bounces at r-project.org> Im Auftrag von Martin
Morgan
Gesendet: Donnerstag, 13. Februar 2020 04:46
An: stefano <mangiolastefano at gmail.com>; bioc-devel at 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 at r-project.org on behalf of mangiolastefano at 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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