On 03/22/2014 01:32 PM, Radford Neal wrote:
From: Philippe GROSJEAN <philippe.grosj...@umons.ac.be>
... for latest CRAN version, we have successfully installed 4999
packages among the 5321 CRAN package on our platform. ... It is
strange that a large portion of R CMD check errors on CRAN occur and
disappear *without any version update* of a package or any of its
direct or indirect dependencies! That is, a fraction of errors or
warnings seem to appear and disappear without any code update.
Some of these are likely the result of packages running tests using
random number generation without setting the random numbers seed, in
which case the seed is set based on the current time and process id,
with an obvious possibility of results varying from run to run.
In the current development version of pqR (in branch 19-mods, found at
https://github.com/radfordneal/pqR/tree/19-mods), I have implemented a
change so that if the R_SEED environment variable is set, the random
seed is initialized to its value, rather than from the time and
process id. This was motivated by exactly this problem - I can now
just set R_SEED to something before running all the package checks.
Beware, if you are serious about reproducing things, that you really
need to save information about the uniform and other generators you use,
such as the normal generator. The defaults do not change often, but have
in the past, and could in the future if something better comes along.
There are some small utilities and examples in the package setRNG which
can help.
Also remember that you need to beware of a side effect of the
environment variable approach. It is great for reproducing things, as
you would want to do in package tests, but be careful how you use it in
functions as it may mess up the randomness if you always set the seed to
the same starting value.
Paul
Radford Neal
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