[BioC] Installing bioconductor under MacOsx

[Jeff Gentry]

On Thu, 1 May 2003, Warnes, Gregory R wrote:
> How are read-only directories handled.  For end-users, it would be ideal if
> they were prompted select which library directory (from the current list)
> should be the installation target.

Well, handled where?  They are handled in several spots, each of which is
in code that has different goals and purposes.

If you mean getBioC() - currently it checks the destdir argument (which
defaults to .libPaths()[1]) and if that does not work it stops and tells
the user to specify a proper destdir.  This would be a place where perhaps
it would be good to put up a menu of all the .libPaths() (assuming that
there's more then 1 - if there's only one, there doesn't seem to be much
point).

Once you get inside reposTools it varies.  Most of these problems (not
necessarily the OP, but a few other people had directory access problems
earlier in the week which was why I had fixed it the other day) stem from
syncLocalLibList() being called automagically at various points in the
reposTools routines.  The intent there is indeed for it to actually go
across all of the .libPaths() and synch each one up.  The "fix" (which is
present in devel and not yet in release) checks for access, and if it does
not exist it throws a warning() and continues down the line of
.libPaths().

Also in reposTools you have the *.packages2() functions - this would seem
to be similar to getBioC in that if it wasn't accesible, that perhaps a
menu would work.  I'm not so sure that this is appropriate here and that
it really should rely on a proper 'lib'/'destDir'/'libs' argument being
specified.  The getBioC() function is intended to be our "user
friendly" installation front end to the reposTools functions, to me this
seems a more appropriate place for things like the menu idea.

-J