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