From krcoombes at mdacc.tmc.edu  Sat Jan 10 00:07:31 2009
From: krcoombes at mdacc.tmc.edu (Kevin R. Coombes)
Date: Fri, 09 Jan 2009 17:07:31 -0600
Subject: [Rd] NY Times article
In-Reply-To: <1231540860.15278.1293959281@webmail.messagingengine.com>
References: <mailman.23.1231498804.5365.r-devel@r-project.org>
	<1231540860.15278.1293959281@webmail.messagingengine.com>
Message-ID: <4967D8B3.7070304@mdacc.tmc.edu>

Hi Nicholas,

You raise a very good point. As an R user (who develops a couple of 
packages for our own local use), I sometimes find myself cringing in 
anticipation of a new R (or BioConductor) release. In my perception 
(which is almost certainly exaggerated, but that's why I emphasize that 
it is only an opinion), clever theoretical arguments in favor of 
structural changes have a tendency to outweigh practical considerations 
of backwards compatibility.

One of my own interests is in "reproducible research", and I've been 
pushing hard here at M.D. Anderson to get people to use Sweave to 
enhance the reproducibility of their own analyses. But, more often than 
I would like, I find that reports written in Sweave do not survive the 
transition from one version of R to the next, because either the core 
implementation or one of the packages they depend on has changed in some 
small but meaningful way.

For our own packages, we have been adding extensive regression testing 
to ensure that the same numbers come out of various computations, in 
order to see the effects of either the changes that we make or the 
changes in the packages we depend on.  But doing this in a nontrivial 
way with real data leads to test suites that take a long time to run, 
and so cannot be incorporated in the nightly builds used by CRAN.

We also encourage our analysts to include a "sessionInfo()" command in 
an appendix to each report so we are certain to document what versions 
of packages were used.

I suspect that the sort of validation you want will have to rely on an 
extensive regression suite test to make certain that the things you need 
remain stable from one release to another. That, and you'll have to be 
slow about upgrading (which may mean foregoing support from the mailing 
lists, where a common refrain in response to bug reports is that "you 
aren't using the latest and greatest version", without an appreciation 
of the fact that there can be good reasons for not changing something 
that you know works....).

Best,
	Kevin

Nicholas Lewin-Koh wrote:
> Hi,
> Kudos, nice exposure, but to make this more appropriate to R-devel I
> would just
> like to make a small comment about the point made by the SAS executive
> about getting
> on an airplane yada yada ...
> 
> 1) It would seem to me that R has certification documents
> 2) anyone designing airplanes, analyzing clinical trials, etc. had 
>    better be worried about a lot more than whether their software is
>    proprietary.
> 
> So from that point of view it would seem that R has made great strides
> over 
> the last 5 years especially in establishing a role for open source
> software solutions in regulated/ commercial
> environments. The question now is how to meld the archiac notions of
> validation and 
> and verification seen in industry with the very different model of open
> source
> development? Rather than the correctness of the software, in which I
> think R is competitive,
> it is how to deal with the rapid release cycles of R, and the
> contributed packages.
> We pull our hair out in pharma trying to figure out how we would ever
> reconcile CRAN and validation requirements. I have no brilliant
> soulution,
> just food for thought
> 
> Nicholas
>  ------------------------------
>> Message: 5
>> Date: Thu, 8 Jan 2009 13:02:55 +0000 (GMT)
>> From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
>> Subject:Re: [Rd]  NY Times article
>> To: Anand Patil <anand.prabhakar.patil at gmail.com>
>> Cc: r-devel at r-project.org
>> Message-ID: <alpine.LFD.2.00.0901081258470.5529 at auk.stats.ox.ac.uk>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>> It has been all over R-help, in several threads.
>>
>> https://stat.ethz.ch/pipermail/r-help/2009-January/184119.html
>> https://stat.ethz.ch/pipermail/r-help/2009-January/184170.html
>> https://stat.ethz.ch/pipermail/r-help/2009-January/184209.html
>> https://stat.ethz.ch/pipermail/r-help/2009-January/184232.html
>> https://stat.ethz.ch/pipermail/r-help/2009-January/184237.html
>>
>> and more
>>
>> On Thu, 8 Jan 2009, Anand Patil wrote:
>>
>>> Sorry if this is spam, but I couldn't see it having popped up on the list
>>> yet.
>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html?emc=eta1
>>>
>>> Anand
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] NY Times article
Kevin R. Coombes