From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Rsquared for reproductible research Date: Thu, 12 Jan 2012 13:33:08 -0700 Message-ID: <87zkdsr797.fsf@gmx.com> References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([140.186.70.92]:37793) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RlRKr-0006gT-Iy for emacs-orgmode@gnu.org; Thu, 12 Jan 2012 15:33:22 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RlRKp-0004k1-7n for emacs-orgmode@gnu.org; Thu, 12 Jan 2012 15:33:21 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:59835) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1RlRKo-0004jb-P7 for emacs-orgmode@gnu.org; Thu, 12 Jan 2012 15:33:19 -0500 In-Reply-To: (brian powell's message of "Thu, 12 Jan 2012 14:44:27 -0500") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: brian powell Cc: emacs-orgmode@gnu.org brian powell writes: >>> Also, I very much agree that a "near exact replica" of the http:// >>> rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great. >> Yes! Any takers?!? >> > ... > Eric questioned: > "From looking at the fairly terse web site for R^2 it is not clear to me > exactly what the system includes (I'm sure I'm missing something > obvious). It seems to be the addition of a packaging system over-top of > R source files. What would a potential Org-mode based system provide > which is not already possible with Org-mode text files, Org-mode > publishing and a version control repository." > ... > > * I mostly agree with your statements. Good challenges. I did more > investigation: This link to the paper that "Friedrich Leischa, , Manuel > Eugsterb, Torsten Hothornb" put together may make things clearer--this > paper really seems to be the justification/impetus for the R^2 website--it > has made things clearer and more exciting for me: > > http://www.sciencedirect.com/science/article/pii/S1877050911001232 > Ah, thank you for linking to this paper. It seems I was missing was the package-management aspect provided by R2 through CRAN. The instillation of all software dependencies is a huge benefit exactly as installing software with apt-get or pacman is simpler than running "./configure && make" and manually resolving dependencies. While such a tool makes sense for a single language system like R, I fear an Org-mode version of such a system would have too wide of a scope. Given that code blocks may contain arbitrary languages, and that sh blocks can freely call any command-line executable such a system would turn into a system-wide package management tool. Perhaps there already exists a portable package management system designed for local installs which could handle most of the heavy lifting. As another option, distributing Virtual Machine images are one solution which I think work well and are increasingly realistic. Or similarly providing the research environment as a cloud server image (e.g., Amazon EC2). Certainly an interesting area for further work! Best, -- Eric Schulte http://cs.unm.edu/~eschulte/