Cheers, after installing Bioconductor on my Debian system I was surprised to see that the new files were installed in the /usr/lib/R tree. Under Debian, this is considered offensive behaviour. Debian assumes that the /usr tree (save /usr/local) is only touched by the distribution, and that non-distributional packages are to be installed in the /usr/local tree. So people who use Debian and related distributions should be advised to change the paths according to their system. Many things run automatically under Bioconductor so sometimes users are tempted to perform things that are not in line with the philosophy of the underlying system. Greetings Johannes

>>>>> "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... Sounds like you installed under root, eh? (or via sudo). Else, you'd get an error. 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).... best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)

Johannnes: You can specify the directory of the lib installation in the "l" parameter of R CMD INSTALL. An example is : R CMD INSTALL -l /xx/yy/zz <downloaded bioconductor=""> Did u try the above method of installation. THis also applies to any R library. Hope this helps. Shyam -----Original Message----- From: Johannes Husig To: bioconductor@stat.math.ethz.ch Sent: 11/29/2002 9:41 AM Subject: [BioC] Installing Biocondutor under Debian r Cheers, after installing Bioconductor on my Debian system I was surprised to see that the new files were installed in the /usr/lib/R tree. Under Debian, this is considered offensive behaviour. Debian assumes that the /usr tree (save /usr/local) is only touched by the distribution, and that non-distributional packages are to be installed in the /usr/local tree. So people who use Debian and related distributions should be advised to change the paths according to their system. Many things run automatically under Bioconductor so sometimes users are tempted to perform things that are not in line with the philosophy of the underlying system. Greetings Johannes _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor