From dwinsemius at comcast.net  Thu Mar 20 07:03:32 2014
From: dwinsemius at comcast.net (David Winsemius)
Date: Wed, 19 Mar 2014 23:03:32 -0700
Subject: [Rd] [RFC] A case for freezing CRAN
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On Mar 19, 2014, at 7:45 PM, Jeroen Ooms wrote:

> On Wed, Mar 19, 2014 at 6:55 PM, Michael Weylandt
> <michael.weylandt at gmail.com> wrote:
>> Reading this thread again, is it a fair summary of your position to say "reproducibility by default is more important than giving users access to the newest bug fixes and features by default?" It's certainly arguable, but I'm not sure I'm convinced: I'd imagine that the ratio of new work being done vs reproductions is rather high and the current setup optimizes for that already.
> 
> I think that separating development from released branches can give us
> both reliability/reproducibility (stable branch) as well as new
> features (unstable branch). The user gets to pick (and you can pick
> both!). The same is true for r-base: when using a 'released' version
> you get 'stable' base packages that are up to 12 months old. If you
> want to have the latest stuff you download a nightly build of r-devel.
> For regular users and reproducible research it is recommended to use
> the stable branch. However if you are a developer (e.g. package
> author) you might want to develop/test/check your work with the latest
> r-devel.
> 
> I think that extending the R release cycle to CRAN would result both
> in more stable released versions of R, as well as more freedom for
> package authors to implement rigorous change in the unstable branch.
> When writing a script that is part of a production pipeline, or sweave
> paper that should be reproducible 10 years from now, or a book on
> using R, you use stable version of R, which is guaranteed to behave
> the same over time. However when developing packages that should be
> compatible with the upcoming release of R, you use r-devel which has
> the latest versions of other CRAN and base packages.


As I remember ... The example demonstrating the need for this was an XML package that cause an extract from a website where the headers were misinterpreted as data in one version of pkg:XML and not in another. That seems fairly unconvincing. Data cleaning and validation is a basic task of data analysis. It also seems excessive to assert that it is the responsibility of CRAN to maintain a synced binary archive that will be available in ten years. Bug fixes would be inhibited for years.... not unlike SAS and Excel. What next? Perhaps al bugs should be labeled as features?  Surely this CRAN-of-the-future would be offering something that no other statistical package currently offers, nicht wahr?

Why not leave it to the authors to specify the packages which version numbers were used in their publications. The authors of the packages would get recognition and the dependencies would be recorded.

-- 
David.
> 
> 
>> What I'm trying to figure out is why the standard "install the following list of package versions" isn't good enough in your eyes?
> 
> Almost nobody does this because it is cumbersome and impractical. We
> can do so much better than this. Note that in order to install old
> packages you also need to investigate which versions of dependencies
> of those packages were used. On win/osx, users need to manually build
> those packages which can be a pain. All in all it makes reproducible
> research difficult and expensive and error prone. At the end of the
> day most published results obtain with R just won't be reproducible.
> 
> Also I believe that keeping it simple is essential for solutions to be
> practical. If every script has to be run inside an environment with
> custom libraries, it takes away much of its power. Running a bash or
> python script in Linux is so easy and reliable that entire
> distributions are based on it. I don't understand why we make our
> lives so difficult in R.
> 
> In my estimation, a system where stable versions of R pull packages
> from a stable branch of CRAN will naturally resolve the majority of
> the reproducibility and reliability problems with R. And in contrast
> to what some people here are suggesting it does not introduce any
> limitations. If you want to get the latest stuff, you either grab a
> copy of r-devel, or just enable the testing branch and off you go.
> Debian 'testing' works in a similar way, see
> http://www.debian.org/devel/testing.
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

David Winsemius
Alameda, CA, USA



[Rd] [RFC] A case for freezing CRAN
David Winsemius