From mboxrd@z Thu Jan  1 00:00:00 1970
From: "Charles C. Berry" <ccberry@ucsd.edu>
Subject: Re: Emacs/ESS/org freezes/hangs on big data/ RAM(~256GB) processes
 when run in org/babel
Date: Fri, 19 Jun 2015 15:13:07 -0700
Message-ID: <alpine.OSX.2.11.1506191505440.914@charles-berrys-macbook.local>
References: <CAOQHXPronGWf70rp7uT_2OjhpBKXvn1m=O2R-rSzk30s_yN4BQ@mail.gmail.com>
	<alpine.DEB.2.02.1506171518001.17579@shell.miskatonic.org>
	<alpine.OSX.2.11.1506171920250.537@charles-berrys-macbook.local>
	<m2lhfhyz3c.fsf@krugs.de>
	<alpine.OSX.2.11.1506181243570.694@charles-berrys-macbook.local>
	<olumvzw90ie.fsf@med.uni-goettingen.de>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Return-path: <emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org>
Received: from eggs.gnu.org ([2001:4830:134:3::10]:43555)
	by lists.gnu.org with esmtp (Exim 4.71)
	(envelope-from <ccberry@ucsd.edu>) id 1Z64XT-000500-N9
	for emacs-orgmode@gnu.org; Fri, 19 Jun 2015 18:13:32 -0400
Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71)
	(envelope-from <ccberry@ucsd.edu>) id 1Z64XQ-0001ne-Go
	for emacs-orgmode@gnu.org; Fri, 19 Jun 2015 18:13:31 -0400
Received: from iport-acv2-out.ucsd.edu ([132.239.0.174]:11531)
	by eggs.gnu.org with esmtp (Exim 4.71)
	(envelope-from <ccberry@ucsd.edu>) id 1Z64XQ-0001nW-7P
	for emacs-orgmode@gnu.org; Fri, 19 Jun 2015 18:13:28 -0400
In-Reply-To: <olumvzw90ie.fsf@med.uni-goettingen.de>
List-Id: "General discussions about Org-mode." <emacs-orgmode.gnu.org>
List-Unsubscribe: <https://lists.gnu.org/mailman/options/emacs-orgmode>,
	<mailto:emacs-orgmode-request@gnu.org?subject=unsubscribe>
List-Archive: <http://lists.gnu.org/archive/html/emacs-orgmode>
List-Post: <mailto:emacs-orgmode@gnu.org>
List-Help: <mailto:emacs-orgmode-request@gnu.org?subject=help>
List-Subscribe: <https://lists.gnu.org/mailman/listinfo/emacs-orgmode>,
	<mailto:emacs-orgmode-request@gnu.org?subject=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: Andreas Leha <andreas.leha@med.uni-goettingen.de>
Cc: emacs-orgmode@gnu.org

On Thu, 18 Jun 2015, Andreas Leha wrote:

> Hi Chuck,
>
> [snip: all context about workflows for R projects]
>
>> For example, the bioConductor package geneRxCluster [1] comes from an
>> Org mode document that contains the C and R code as src blocks and a
>> subtree with the vignette (Using geneRxCluster) that analyzes data,
>> produces graphics, etc. tangle-ing the src blocks and exporting the
>> vignette creates the package.
>>
>
> I'd love to see that org document, but I do not seem to be able to find
> it.  Is it available anywhere?

Andreas,

It is now, or at least the relevant subset of it is at:

https://github.com/chasberry/geneRx/blob/master/Rpackage.org

It is best viewed in Org mode as there are internal links that github does 
not honor (so you get `404 This is not...' messages if you click on them).

And it is best to use those internal links as the file was not designed to 
be read from top to bottom - it has lots of snippets I used to develop and 
check code along the way that are not in the actual package and I have 
left them in place.

Best,

Chuck