library path in Rd link

Dear Prof. Ripley,

On Wednesday 14 November 2007, Prof Brian Ripley wrote:

On Wed, 14 Nov 2007, Adrian Dusa wrote:

Dear all,

When creating new functions in a package, there is a "See also" component
in the Rd file.
Usually one uses \link{otherfun}, if the other function is from the same
package, or \link[otherpackage]{otherfun} otherwise.

I think you have misread the manual here:

   There are two other forms of optional argument specified as
   \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to
   files foo.html and bar.html respectively. These are rarely needed,
   perhaps to refer to not-yet-installed packages (but there the HTML
   help system will resolve the link at run time) or in the normally
   undesirable event that more than one package offers help on a topic
   (in which case the present package has precedence so this is only
   needed to refer to other packages)

Note: 'rarely needed'.

Ah-haa, thanks for the clarification. I could have directly used
\code{\link{anova}}
to refer to the anova() from package stats which is also installed by default
in the same installation folder as the base package.

The trouble is that I install new packages not in the default R library
folder, but into some other subfolder in my home, so the link searches
for "otherpackage" in my home subfolder.

Is there a method to create links to functions from the base package, for
example (which is installed by default in the normal library folder)?

What OS is this?  (As I recall you used Linux last time you posted.)

Linux it is, I only thought the question should be platform independent.

In any case, on all OSes you will be able to do cross-library links to the
base package without having to do anything further (and CRAN packages are
full of them).  On Unix-alikes the help files are all linked into a single
virtual library, and on Windows links to the base package (and a few
others) from other libraries are fixed up on installation by
link.html.help (see its help).

Indeed, link.html.help() resolves all the links under Windows (where I
suspected the biggest trouble would be). It is strangely under Linux that I
am not able to resolve the links (most surely I do something wrong).

Using as above:
\code{\link{anova}}

the html help file directs to
file:///home/adi/myRlibrary/stats/html/anova.html

instead of
file:///usr/lib/R/library/stats/html/anova.html

help.start()

help("anova", htmlhelp=TRUE)