[BioC] alias in .Rd and bundles

[Kurt Hornik]

>>>>> Sandrine Dudoit writes:

> Hello,

> I have a couple of R questions.

> 1. When we have several aliases in a .Rd file is there a way to have only
> the first alias listed in the index for the package (00Index.html)
> I am asking this especially in the context of the marrayClasses package
> for the .Rd files for the classes. The index now lists both
> marrayLayout and marrayLayout-class. We added the alias marrayLayout because
> it's easier for people to use ? marrayLayout than ?
> marrayLayout-class.

Sandrine,

That's a limitation of the current Rd system: the INDEX file is
generated from the info in the *name* and title slots of the Rd file.
[This was not too bad in the old days but is really braindead now that
we even say that the name is just an id which must be unique across the
Rd objs in the package].  The \alias info is currently not used.

R 1.6 should have a 3-arg \index command along the lines of

	\index{TOPIC}{TYPE}{DESCRIPTION}
or
	\index[TYPE]{TOPIC}{DESCRIPTION}

the latter being my pref, which will allow us to have a real index
system.  For the time being, all you can do is split into small pieces,
or write good vignettes so that no one needs to look at the INDEX
files.

-k