On Wed, 11 Jun 2008, Bill Dunlap wrote:
On Wed, 11 Jun 2008, Kevin R. Coombes wrote:
[1] Because of the need for a nightly build of BioConductor, the tests
(in the ./tests directory) of a package that run routinely as part of "R
CMD check" must complete in five minutes.
[2] Nontrivial regression testing of complex algorithms on real data can
easily take longer than five minutes.
[3] Maintaining and improving code that works on various kinds of
"omics" data is greatly facilitated by the inclusion of nontrivial
regression tests.
Of course, points [1] and [3] are incompatible in the current setup.
Both could, however, be accommodated by changing the way "R CMD check"
runs test scripts. There are at least two ways this could be accomplished.
Another approach is to have check use the new-to-2.8.0 function
setSessionTimeLimit() to let the checker put a time limit on
the tests. In a time-constrained environment you could ask check
to spend no more than 5 minutes running the tests but you could
also set the limit to 3 hours or Inf or anything else.
This would only be useful if the quicker tests were done first,
so you'd have to alphabetize your test files.
Or to use environment variable(s) to select which tests to do (which is
what I had started to write a reply to suggest when I got diverted to
something more urgent). E.g. 'foreign' has a slow test that needs
Internet access, and it will become optional via an environment variable
in the next release.
BTW, some of us run checks with a Unix-level time limit set: there are a
few CRAN packages that infinite-loop on 64-bit systems so it is a
necessary precaution.
It might be nice if check could print the time it took to do
each test.
That's an existing request for various parts of the checking procedure.
When the time to run a package check jumps up, it is sometimes tedious to
find out where the time went. But the tests are currently scripted by
make, so difficult to produce timings portably.
Bill Dunlap
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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