[Bioc-devel] R cmd check time limits for BioConductor

Hi,

I have considered that possibility, but am not yet convinced that it is 
the best approach. I will, of course, do something like that if I cannot 
persuade this list that an alternative approach might be better. The 
basic argument is:

* Complex algorithms can be better maintained if they are accompanied by 
regression testing.
* "R CMD check" provides an automated method to run regression tests, 
with a defined directory structure for storing those tests.
* Changing the directory location in the source makes running the 
regression tests more awkward and thus less likely to occur on a regular 
basis.
* The "--no-tests" argument already provides a mechanism for preventing 
the tests from being run.

What appears to be missing is either a mechanism to designate the tests 
as optional or to indicate a preference for not running some or all of 
them. I can think of three ways to accomplish my goals in this matter:

[1] Make "--no-tests" the default way to run "R CMD check" at 
BioConductor. (Of course, this is unlikely to be the optimal solution 
since it merely avoids the question.)
[2] Add a field to the DESCRIPTION file that tells "R CMD check" whether 
or not to run the tests. Something like
	Tests: run
or
	Tests: dontrun
[3] Add an optional special file in the tests directory that indicates 
the complexity/length of the tests that would allow "R CMD check" to 
decide whether or not to run them. Perhaps something like

###################
# COMPLEXITY file

test1.R: long
test2.R: short
...
###################

Of course, options [2] or [3] require changes to "R CMD check" (for 
which I should eventually move this discussion to the R-devel list), but 
I am really only interested in convincing BioConductor that (possibly 
complex) regression tests are a good thing, and should be encouraged by 
adopting something like [1].

Best,
	Kevin

2008/6/10 Kevin R. Coombes <krcoombes at mdacc.tmc.edu>:

Hi,

The BioConductor package guidelines say that a package should take less than
five minutes to run "R CMD check". I have a package that is almost ready to
submit; however, it currently includes nontrivial regression testing in the
"tests" subdirectory. With the tests, the time for "R CMD check" could be
significantly longer than five minutes. Without the tests, the package
easily fits within the time limit.

[1] I know that I can run "R CMD check --no-tests [PKG]" to prevent the
tests from running when I check the code myself. Is there any way for a
package submitted to BioConductor to indicate that the tests should be
skipped?

[2] Alternatively, is there an easy way to include the tests so that I can
run them whenever I want to make sure I haven't broken the code (too badly
...), but not force everyone else to run them when checking the rest of the
structure of the code and documentation?

You could consider having them in your package, in a directory
inst/tests/ for example
(so the tests are still available from an installed package).

Thanks in advance,
   Kevin

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