R help - Sep 2009 - Missing link(s) in documentation object

Hi,

I want to cross-reference from the documentation of pkg1 to pkg2, which 
is imported in the NAMESPACE of pkg1, and under Depends in DESCRIPTION 
of pkg1. According to "Writing R extensions", this can be done by:
\code{\link{foo}}
when foo is an aliased function in the documentation of pkg2. This works 
as it should when I install the package, but when I run R CMD check 
pgk1, I get a warning:

* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'fooPkg1.Rd'
  foo

I have tried to change the link to
\code{\link[pkg2]{foo}}
\code{\link[pkg:pkg2]{foo}}
None of these works, the first gives a link that leads to an error page, 
and the second one gives a link that does not work at all. I assume this 
is as it should be; foo.Rd does not exist. However, R CMD check does not 
complain about any of these links...

Why does R CMD check warn me against links that work? I think pkg2 is 
not on the search path when looking for cross-references, but why? R CMD 
check continues to run after the warning without any complaints, and all 
tests rely on pkg2. I am quite sure there is something simple that I 
have overlooked, but cannot figure out what it is.

Best wishes,
Jon

Platform etc:
XP SP3, R 2.9-2, Rtools210 (the problem was also there before upgrading 
from R 2.9-1 and Rtools29 )

Jon Olav Skoien wrote:
> Hi,
> 
> I want to cross-reference from the documentation of pkg1 to pkg2, which
> is imported in the NAMESPACE of pkg1, and under Depends in DESCRIPTION
> of pkg1. According to "Writing R extensions", this can be done
by:
> \code{\link{foo}}
> when foo is an aliased function in the documentation of pkg2. This works
> as it should when I install the package, but when I run R CMD check
> pgk1, I get a warning:
> 
> * checking Rd cross-references ... WARNING
> Missing link(s) in documentation object 'fooPkg1.Rd'
>  foo
> 
> I have tried to change the link to
> \code{\link[pkg2]{foo}}
> \code{\link[pkg:pkg2]{foo}}
Hi Jon --

I think the current requirement is \link[pkg2;foo_Rd_file_name]{foo}
where foo_Rd_file_name  is the name (without the .Rd extension) of the
FILE in which foo is documented. This would appear not to be foo.Rd,
because you say \link[pkg2]{foo} fails. This is as documented in Writing
R extensions.
> None of these works, the first gives a link that leads to an error page,
> and the second one gives a link that does not work at all. I assume this
> is as it should be; foo.Rd does not exist. However, R CMD check does not
> complain about any of these links...
Try building with R-devel, where the error messages are more detailed.
> Why does R CMD check warn me against links that work? I think pkg2 is
I think the idea is that the cross-package links as you originally
specified work for some help formats, but not for others (e.g., pdf).

Martin
> not on the search path when looking for cross-references, but why? R CMD
> check continues to run after the warning without any complaints, and all
> tests rely on pkg2. I am quite sure there is something simple that I
> have overlooked, but cannot figure out what it is.
> 
> Best wishes,
> Jon
> 
> Platform etc:
> XP SP3, R 2.9-2, Rtools210 (the problem was also there before upgrading
> from R 2.9-1 and Rtools29 )
> 
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