From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1OhmlV-0002tg-3K for garchives@archives.gentoo.org; Sat, 07 Aug 2010 17:00:57 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 17D16E0803; Sat, 7 Aug 2010 17:00:25 +0000 (UTC) Received: from smtp.webfaction.com (mail6.webfaction.com [74.55.86.74]) by pigeon.gentoo.org (Postfix) with ESMTP id DF77EE0803 for ; Sat, 7 Aug 2010 17:00:24 +0000 (UTC) Received: from mail-qy0-f174.google.com (mail-qy0-f174.google.com [209.85.216.174]) by smtp.webfaction.com (Postfix) with ESMTP id 473FA324172 for ; Sat, 7 Aug 2010 12:00:24 -0500 (CDT) Received: by qyk7 with SMTP id 7so737402qyk.19 for ; Sat, 07 Aug 2010 10:00:23 -0700 (PDT) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-Version: 1.0 Received: by 10.224.116.18 with SMTP id k18mr7114158qaq.303.1281200422821; Sat, 07 Aug 2010 10:00:22 -0700 (PDT) Received: by 10.229.21.135 with HTTP; Sat, 7 Aug 2010 10:00:22 -0700 (PDT) Date: Sat, 7 Aug 2010 19:00:22 +0200 Message-ID: Subject: [gentoo-science] G-CRAN works, testing needed From: Auke Booij To: gentoo-science@lists.gentoo.org, brian.dolbec@gmail.com, =?ISO-8859-1?Q?S=E9bastien_Fabbro?= Content-Type: text/plain; charset=ISO-8859-1 X-Archives-Salt: 1c8b6f02-8ab0-4927-a6c5-bb098e7cc1c5 X-Archives-Hash: 874d95191ab65a3e86e50866444aa857 Hi there, fellow scientists! So I guess that if you haven't lived under a rock for the past few months (and did not recently join gentoo-science), you have probably heard about my efforts to help y'all install R extension packages (CRAN and bioconductor are the obvious targets, since they are the most popular R package repositories). My project is pretty much complete now, and I'd like to tell you how to use my code and start using R packages. Now, I solved the problem slightly differently from packages like g-cpan and g-octave. Instead of generating ebuilds as they are needed, I've written another package called g-common which gives us transparent access to non-ebuild package repositories (although currently only R repos and PEAR are supported). To make our life even easier, I've written a layman patch to be able to access R package repositories just like we would access a regular ebuild overlay. The code is not in portage yet, of course, so this is how you install, as a simple example, the "zoo" package from CRAN: -add the kuroo and science overlays if you don't have them yet -install =layman-8888 from kuroo and g-cran from science (g-common is currently included in g-cran) -save the attached repositories.xml to /var/lib/repositories.xml (or whatever you think is appropriate) -edit /etc/layman/layman.cfg and add file:///var/lib/repositories.xml to "overlays" (on its own line) -layman -a CRAN -emerge -av dev-R/zoo For your convenience, I also added the bioconductor repositories to repositories.xml. If you'd like to try these, please note that the "annotation" part of bioconductor depends on the "bioc" part (and all the gene databases and stuff are in "annotation", so you'll probably want to get both). Please test packages, and tell me about everything that you think could be improved. Build errors, usability problems... tell me what you think, so that we can make Gentoo the first distribution which can directly install non-native packages using the package manager! Should you have any questions or remarks, you can often find me on IRC (#gentoo-soc, #gentoo-science, or just privmsg me), but I regularly read my email too. Auke Booij / tulcod.