[BioC] Installing Biocondutor under Debian r
Johannes Hüsing
johannes.huesing@ruhrau.de
Sun, 1 Dec 2002 11:54:44 +0100
On Fri, Nov 29, 2002 at 05:28:41PM -0800, A.J. Rossini wrote:
> >>>>> "johannes" == Johannes Husig <derwisch@panix.com> writes:
>
> johannes> Cheers,
> johannes> after installing Bioconductor on my Debian system I was
> johannes> surprised to see that the new files were installed in
> johannes> the /usr/lib/R tree.
>
> johannes> Under Debian, this is considered offensive behaviour.
> johannes> Debian assumes that the /usr tree (save /usr/local) is
> johannes> only touched by the distribution, and that non-distributional
> johannes> packages are to be installed in the /usr/local tree.
>
> johannes> So people who use Debian and related distributions should
> johannes> be advised to change the paths according to their system.
>
> johannes> Many things run automatically under Bioconductor so sometimes
> johannes> users are tempted to perform things that are not in line with
> johannes> the philosophy of the underlying system.
>
>
> This is actually true of ANY R INSTALL under the Debian system, unless
> you specify a local install. Doesn't matter if it's Bioconductor or
> not! It is a well known problem to the Debian maintainer, and
> discussion as to the "right" solution is still on going...
>
Yep, it's a bit like TeX, where distributions are nicely packaged which
makes a re-packaging by the Debian distribution slightly redundant. I can
sense a problem where the solution is not trivial.
> Sounds like you installed under root, eh? (or via sudo). Else, you'd
> get an error.
Yes.
>
> I've got Debian packages for Bioconductor (takes care of some of the
> associated requirements, such as PostgreSQL for AnnBuilder, etc).
> I'll make the archive available as soon as they get vetted by a
> developer I've been working with (the debian R maintainer)....
That'd be very helpful. Thanks a lot!
Greetings
Johannes
--
Johannes Hüsing There is something fascinating about science. One gets
hannes@ruhrau.de such wholesale returns of conjecture from such a
trifling investment of fact. Mark Twain