[Bioc-devel] linking to suggested package in documentation

[Stephanie M. Gogarten]

The package is installed on my system.  If it is listed in the 
"Suggests" field, I get the warning

* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 
‘/Volumes/geneva_sata/stephanie/Bioconductor/GWASTools/man/snpStats.Rd’:
   ‘SnpMatrix-class’

If I move the "snpStats" package from "Suggests" to "Imports," that 
warning goes away.

I can see why R would warn about documentation links to packages in 
"Suggests", because if the package is not installed the link would be 
broken.  But I was wondering if there was a clever way to convince R CMD 
check that packages in "Suggests" should be considered valid for 
documentation links.

thanks,
Stephanie

On 5/17/12 3:00 AM, bioc-devel-request at r-project.org wrote:
> Date: Thu, 17 May 2012 08:30:45 +0900 From: "Y-h. Taguchi"
> <tag at granular.com> To: bioc-devel at r-project.org Subject: Re:
> [Bioc-devel] linking to suggested package in documentation Message-ID:
> <CAJgr72=p9-13BBseFNwGR_nDGv0-2QSvhcbH+4oWwHb9R42Dtw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-2022-JP Dear Steohanie, 2012/5/17
> Stephanie M. Gogarten <sdmorris at u.washington.edu>:
>> >  Is is possible to include a link to a package/function/class in the
>> >  documentation if that package is only listed in "Suggests" rather than
>> >  "Depends" or "Imports"?
> Yes, you can, but....
>
>> >I tried to do this, but I got a warning for a
>> >  missing link during R CMD check.
> In order to run "R CMD check" properly, you need to install everything
> in  Suggests","Depends" or "Imports" in your ssytem, since it tries to
> execute every example in vignette.
>
> Have you tried it?
>
> yours, tag.
>
>> >
>> >  Stephanie
>> >
>> >  _______________________________________________
>> >  Bioc-devel at r-project.org  mailing list
>> >  https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> -- Y-h. Taguchi, Dept. Phys., Chuo Univ., Kasuga, Bunkyo-ku, Tokyo
> 112-8551,Japan Tel./Fax. +81-3-3817-1791/1792
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