On 03/20/2014 03:29 PM, Uwe Ligges wrote:
On 20.03.2014 23:23, Hervé Pagès wrote:
On 03/20/2014 01:28 PM, Ted Byers wrote:
On Thu, Mar 20, 2014 at 3:14 PM, Hervé Pagès <hpa...@fhcrc.org
<mailto:hpa...@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" <dwinsem...@comcast.net
<mailto:dwinsem...@comcast.net>>
To: "Jeroen Ooms" <jeroen.o...@stat.ucla.edu
<mailto:jeroen.o...@stat.ucla.edu>>
Cc: "r-devel" <r-devel@r-project.org
<mailto:r-devel@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.weyla...@gmail.com
<mailto:michael.weyla...@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.
Not true, since Matrix 1.1-2-2 has
Depends: R (≥ 2.15.2)
OK. So that means Matrix is not available today for R-2.13.2 users on
Linux:
> "Matrix" %in% rownames(available.packages()[ , ])
[1] FALSE
However since Matrix is a recommended package, it's included in
the official R-2.13.2 source tarball so it gets installed when I
install R:
> installed.packages()["Matrix", "Version", drop=FALSE]
Version
Matrix "0.9996875-3"
As I mentioned earlier, the Matrix package was just an example. In the
case of a non-recommended package, it will either be:
- unavailable by default (if the source package was removed or if
the package maintainer consciously used the R >= x.y.z feature,
e.g. the ape package),
- or available but incompatible (e.g. bcrm is broken with R-2.13.2
on Linux),
- or available and compatible, but with a very different version
than the version that was available 2 years ago (e.g. BaSTA),
- or available and at the exact same version as 2 years ago (bingo!)
This is a very painful experience for anybody trying to install and
use R-2.13.2 today to reproduce 2-year old results. Things could be
improved a lot with very little changes.
Cheers,
H.
> sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.13.2
Best,
Uwe Ligges
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 3.16.2.3 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?
Cheers,
H.
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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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