[Rd] [RFC] A case for freezing CRAN

Hervé Pagès hpages at fhcrc.org
Thu Mar 20 23:23:57 CET 2014

On 03/20/2014 01:28 PM, Ted Byers wrote:
> On Thu, Mar 20, 2014 at 3:14 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>> wrote:
>     On 03/20/2014 03:52 AM, Duncan Murdoch wrote:
>         On 14-03-20 2:15 AM, Dan Tenenbaum wrote:
>             ----- Original Message -----
>                 From: "David Winsemius" <dwinsemius at comcast.net
>                 <mailto:dwinsemius at comcast.net>>
>                 To: "Jeroen Ooms" <jeroen.ooms at stat.ucla.edu
>                 <mailto:jeroen.ooms at stat.ucla.edu>>
>                 Cc: "r-devel" <r-devel at r-project.org
>                 <mailto:r-devel at r-project.org>>
>                 Sent: Wednesday, March 19, 2014 11:03:32 PM
>                 Subject: Re: [Rd] [RFC] A case for freezing CRAN
>                 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
>                     <mailto: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.
>             CRAN already does this, the bin/windows/contrib directory has
>             subdirectories going back to 1.7, with packages dated
>             October 2004. I
>             don't see why it is burdensome to continue to archive these.
>             It would
>             be nice if source versions had a similar archive.
>         The bin/windows/contrib directories are updated every day for
>         active R
>         versions.  It's only when Uwe decides that a version is no
>         longer worth
>         active support that he stops doing updates, and it "freezes".  A
>         consequence of this is that the snapshots preserved in those older
>         directories are unlikely to match what someone who keeps up to
>         date with
>         R releases is using.  Their purpose is to make sure that those older
>         versions aren't completely useless, but they aren't what Jeroen was
>         asking for.
>     But it is almost completely useless from a reproducibility point of
>     view to get random package versions. For example if some people try
>     to use R-2.13.2 today to reproduce an analysis that was published
>     2 years ago, they'll get Matrix 1.0-4 on Windows, Matrix 1.0-3 on Mac,
>     and Matrix 1.1-2-2 on Unix. And none of them of course is what was used
>     by the authors of the paper (they used Matrix 1.0-1, which is what was
>     current when they ran their analysis).
> Initially this discussion brought back nightmares of DLL hell on
> Windows.  Those as ancient as I will remember that well.  But now, the
> focus seems to be on reproducibility, but with what strikes me as a
> seriously flawed notion of what reproducibility means.
> Herve Pages mentions the risk of irreproducibility across three minor
> revisions of version 1.0 of Matrix.

If you use R-2.13.2, you get Matrix 1.1-2-2 on Linux. AFAIK this is
the most recent version of Matrix, aimed to be compatible with the most
current version of R (i.e. R 3.0.3). However, it has never been tested
with R-2.13.2. I'm not saying that it should, that would be a big waste
of resources of course. All I'm saying it that it doesn't make sense to
serve by default a version that is known to be incompatible with the
version of R being used. It's very likely to not even install properly.

For the apparently small differences between the versions you get on
Windows and Mac, the Matrix package was just an example. With other
packages you get (again if you use R-2.13.2):

               src   win    mac
   abc         1.8   1.5    1.4
   ape       3.1-1 3.0-1    2.8
   BaSTA     1.9.3   1.1    1.0
   bcrm      0.4.3   0.2    0.1
   BMA  3.15 3.14.1
   Boruta    3.0.0   1.6    1.5

Are the differences big enough?

Also note that back in October 2011, people using R-2.13.2 would get
e.g. ape 2.7-3 on Linux, Windows and Mac. Wouldn't it make sense that
people using R-2.13.2 today get the same? Why would anybody use
R-2.13.2 today if it's not to run again some code that was written
and used two years ago to obtain some important results?


> My gut reaction would be that if
> the results are not reproducible across such minor revisions of one
> library, they are probably just so much BS.  I am trained in
> mathematical ecology, with more than a couple decades of post-doc
> experience working with risk assessment in the private sector.  When I
> need to do an analysis, I will repeat it myself in multiple products, as
> well as C++ or FORTRAN code I have hand-crafted myself (and when I wrote
> number crunching code myself, I would do so in multiple programming
> languages - C++, Java, FORTRAN, applying rigorous QA procedures to each
> program/library I developed).  Back when I was a grad student, I would
> not even show the results to my supervisor, let alone try to publish
> them, unless the results were reproducible across ALL the tools I used.
> If there was a discrepancy, I would debug that before discussing them
> with anyone.  Surely, it is the responsibility of the journals' editors
> and reviewers to apply a similar practice.
> The concept of reproducibility used to this point in this discussion
> might be adequate from a programmers perspective (except in my lab), it
> is wholly inadequate from a scientist's perspective.  I maintain that if
> you have the original data, and repeat the analysis using the latest
> version of R and the available, relevant packages, the original results
> are probably due to a bug either in the R script or in R or the packages
> used IF the results obtained using the latest versions of these are not
> consistent with the originally reported results.  Therefore, of the
> concerns I see raised in this discussion, the principle one of concern
> is that of package developers who fail to pay sufficient attention to
> backwards compatibility: a new version ought not break any code that
> executes fine using previous versions.  That is not a trivial task, and
> may require contributors obtaining the assistance of a software
> engineer.  I am sure anyone in this list who programs in C++ knows how
> the ANSI committees handle change management.  Introduction of new
> features is something that is largely irrelevant for backwards
> compatibility (but there are exceptions), but features to be removed
> are handled by declaring them deprecated, and leaving them in that
> condition for years.  That tells anyone using the language that they
> ought to plan to adapt their code to work when the deprecated feature is
> finally removed.
> I am responsible for maintaining code (involving distributed computing)
> to which many companies integrate their systems, and I am careful to
> ensure that no change I make breaks their integration into my system,
> even though I often have to add new features.  And I don't add features
> lightly, and have yet to remove features.  When that eventually happens,
> the old feature will be deprecated, so that the other companies have
> plenty of time to adapt their integration code.  I do not know whether
> CRAN ought to have any responsibility for this sort of change
> management, or if they have assumed some responsibility for some of it,
> but I would argue that the package developers have the primary
> responsibility for doing this right.
> Just my $0.05 (the penny no longer exists in Canada)
> Cheers
> Ted
> R.E. (Ted) Byers, Ph.D., Ed.D.

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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