From romain at r-enthusiasts.com  Thu Mar 20 01:13:03 2014
From: romain at r-enthusiasts.com (Romain Francois)
Date: Thu, 20 Mar 2014 01:13:03 +0100
Subject: [Rd] [RFC] A case for freezing CRAN
In-Reply-To: <532A20D7.2010905@fhcrc.org>
References: <CABFfbXt0PjHEw-4=VfeWeeosm_wOBH-fVsj85j9LMe81Lx0gWQ@mail.gmail.com>	<53299314.6080608@gmail.com>	<CABFfbXuTvefJ0Nmc25JJEwhmUQge+K1Fi=oaTwoO_jfK75mUZg@mail.gmail.com>	<CAPPM_gRP4xKEE1bFiR8Aaeo1XOX0kpu4p=EyOm2z+6fkVkJaag@mail.gmail.com>	<CABFfbXtmFyoyaRSU6LyWrUzyXvvkSV14yD3vc0c2fzRcHbtNzQ@mail.gmail.com>
	<CAPPM_gR7pP7eq2Gg3nT4osSw1S69hvEW=yCx3-Q7T1V0fb19Vg@mail.gmail.com>
	<532A20D7.2010905@fhcrc.org>
Message-ID: <ED1036A5-FCB2-4F8A-B635-72957B6E7FAA@r-enthusiasts.com>

Weighting in. FWIW, I find the proposal conceptually quite interesting. 

For package developers, it does not have to be a frustration to have to wait a new version of R to release their code. Anticipated frustration was my initial reaction. Thinking about this more, I think this could be changed into opportunity. 

Since the pattern here is to use Rcpp as an example of something causing compatibility headaches, and I have some responsibility there, maybe I can comment on this. I would find it extremely valuable if there was only one unique version of Rcpp for a given released version of R. 

Users would have to wait longer to have the new stuff, but one can argue that at least they get something that is more tested. 

Would it be helpful for authors of package that have lots of dependency to start having stricter depends declarations in their DESCRIPTION files, e.g. : 

Depends: R (== 3.1.0)

?

Romain


For example, personally I?m waiting for 3.1.0 for releasing Rcpp11 because I want to leverage some C++11 support that has been included in R. It has been frustrating to have to wait, but it does change the way I make changes to the codebase. Perhaps it is a good habit to take. And it does not need ? more work ? for others, just more discipline and self control from people implementing this pattern. 

also, declaring a strict dependency requirement against a released version of R perhaps could resume the drama of ? you were asked to test this against a very recent version of R-devel, and guess what a few hours ago I?ve just added a new test that makes your package non R CMD check worthy ?. So less work for CRAN maintainers then. 

Le 19 mars 2014 ? 23:57, Herv? Pag?s <hpages at fhcrc.org> a ?crit :

> 
> 
> On 03/19/2014 02:59 PM, Joshua Ulrich wrote:
>> On Wed, Mar 19, 2014 at 4:28 PM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
>>> On Wed, Mar 19, 2014 at 11:50 AM, Joshua Ulrich <josh.m.ulrich at gmail.com>
>>> wrote:
>>>> 
>>>> The suggested solution is not described in the referenced article.  It
>>>> was not suggested that it be the operating system's responsibility to
>>>> distribute snapshots, nor was it suggested to create binary
>>>> repositories for specific operating systems, nor was it suggested to
>>>> freeze only a subset of CRAN packages.
>>> 
>>> 
>>> IMO this is an implementation detail. If we could all agree on a particular
>>> set of cran packages to be used with a certain release of R, then it doesn't
>>> matter how the 'snapshotting' gets implemented. It could be a separate
>>> repository, or a directory on cran with symbolic links, or a page somewhere
>>> with hyperlinks to the respective source packages. Or you can put all
>>> packages in a big zip file, or include it in your OS distribution. You can
>>> even distribute your entire repo on cdroms (debian style!) or do all of the
>>> above.
>>> 
>>> The hard problem is not implementation. The hard part is that for
>>> reproducibility to work, we need community wide conventions on which
>>> versions of cran packages are used by a particular release of R. Local
>>> downstream solutions are impractical, because this results in
>>> scripts/packages that only work within your niche using this particular
>>> snapshot. I expect that requiring every script be executed in the context of
>>> dependencies from some particular third party repository will make
>>> reproducibility even less common. Therefore I am trying to make a case for a
>>> solution that would naturally improve reliability/reproducibility of R code
>>> without any effort by the end-user.
>>> 
>> So implementation isn't a problem.  The problem is that you need a way
>> to force people not to be able to use different package versions than
>> what existed at the time of each R release.  I said this in my
>> previous email, but you removed and did not address it: "However, you
>> would need to find a way to actively _prevent_ people from installing
>> newer versions of packages with the stable R releases."  Frankly, I
>> would stop using CRAN if this policy were adopted.
>> 
>> I suggest you go build this yourself.  You have all the code available
>> on CRAN, and the dates at which each package was published.  If others
>> who care about reproducible research find what you've built useful,
>> you will create the very community you want.  And you won't have to
>> force one single person to change their workflow.
> 
> Yeah we've already heard this "do it yourself" kind of answer. Not a
> very productive one honestly.
> 
> Well actually that's what we've done for the Bioconductor repositories:
> we freeze the BioC packages for each version of Bioconductor. But since
> this freezing doesn't happen at the CRAN level, and many BioC packages
> depend on CRAN packages, the freezing is only at the surface. Would be
> much better if the freezing was all the way down to the bottom of the
> sea. (Note that it is already if you install binary packages only.)
> 
> Yes it's technically possible to work around this by also hosting
> frozen versions of CRAN, one per version of Bioconductor, and have
> biocLite() (the tool BioC users use for installing packages) point to
> these frozen versions of CRAN in order to get the correct dependencies
> for any given version of BioC. However we don't do that because that
> would mean extra costs for us in terms of storage space and bandwidth.
> And also because we believe that it would be more effective and would
> ultimately benefit the entire R community (and not just the BioC
> community) if this problem was addressed upstream.
> 
> H.
> 
>> 
>> Best,
>> --
>> Joshua Ulrich  |  about.me/joshuaulrich
>> FOSS Trading  |  www.fosstrading.com
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
> 
> -- 
> Herv? Pag?s
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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> 
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[Rd] [RFC] A case for freezing CRAN
Romain Francois