Re: [Rd] library path in Rd link

From: Prof Brian Ripley <>
Date: Wed, 14 Nov 2007 23:21:39 +0000 (GMT)

On Thu, 15 Nov 2007, Adrian Dusa wrote:

> 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
>> (see its help).
> Indeed, 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

I hope it is actually ../../stats/html/anova.html and the browser is interpreting that as a full URL.

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

But at run time help.start() creates links into a subdirectory of tempdir(). As in

> help.start()

Making links in per-session dir ...
If '/home/ripley/bin/firefox' is already running, it is *not*

     restarted, and you must switch to its window. Otherwise, be patient ...

and without that

> help("anova", htmlhelp=TRUE)

Help for 'anova' is shown in browser /home/ripley/bin/firefox ... Use

         help("anova", htmlhelp = FALSE) or

         options(htmlhelp = FALSE)
to revert.
Warning message:
In .show_help_on_topic_as_HTML(file, topic) :

   Using non-linked HTML file: style sheet and hyperlinks may be incorrect

and note the last line.

(In case anyone wonders about the browser path: I am running 32-bit Firefox on x86_64 Linux.)

Brian D. Ripley,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

______________________________________________ mailing list
Received on Wed 14 Nov 2007 - 23:28:19 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 15 Nov 2007 - 00:30:18 GMT.

Mailing list information is available at Please read the posting guide before posting to the list.