[Bioc-devel] linking to suggested package in documentation

[Martin Morgan]

On 05/17/2012 08:16 AM, Stephanie M. Gogarten wrote:
> 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.

Hi Stephanie --

I think you're looking for sectin 2.5 of Writing R Extensions -- Cross 
references, along the lines of

   \link[pkg]{foo}

where 'foo' is the name of the _html_ file foo is documented in, or

   \link[pkg:bar]{foo}

to find documentation on foo in html page bar.html.

Martin

>
> 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
>> http://www.granular.com/tag/index-j.html ?112-8551 ???????? ???? ????
>> ??/FAX 03-3817-1791/1792
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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