Sorry if there's an obvious answer to this, that I've missed, but what
are people doing with respect to licenses for their packages, and
disclaimers and stuff like that?
In the end, it is really up to the package author.
The general policy for Bioconductor is that packages that are intended to
be more infrastructure oriented are preferred to be under something on the
less restrictive side (e.g. LGPL is a common one, BSD is certainly 'less
restrictive'), but as I said, at this point at least - it is really up to
the authors, we haven't really gotten into the business of managing all of
the potential license choices.
One potential issue is if someone has put a more restrictive license on
their package, e.g. "for educational use only" or something like
that. When this issue was last discussed (and I'm sure I'll be corrected
here if I'm wrong), my understanding was that we'd still distribute it as
any other package and any potential licensing issues are between the
author/maintainer and the downloader.
For my own personal side, I use LGPL for the packages that I author (I
believe we have one or two BSD licensed packages, and perhaps a small
handful of other 'other licenses' but the rest are some mix of LGPL and
GPL) simply due to philosophical issues I have against the proper GPL, but
as I said twice already - it is really up to the author :)