[BioC] alias in .Rd and bundles

[Sandrine Dudoit]

Hi Kurt,

Thanks for the reply.

> > 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.


I meant the html index in /html/00Index.html. This ones seems to be using
the alias and adds an entry for each aliased name.

Best,
Sandrine