[Bioc-devel] linking to suggested package in documentation

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

-- 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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