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

[Felix Ernst]

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
    
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