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

Kevin R. Coombes krcoombes at mdacc.tmc.edu
Wed Jun 11 15:47:18 CEST 2008

Hi Vince,

I agree with everything you said. The conclusion I draw from it (which 
is, of course, compatible with my prior distribution on the issue ...) 
is that we really need two levels of testing. One would cover your 
issues (1) and (2) and, because of the need to complete checking and 
building every day, would have to run quickly. A more elaborate level of 
systematic "deep" regression testing should also be available which (i) 
would not be run by default but (ii) could be optionally included by "R 
CMD check" without forcing everyone who wants this kind of testing to 
have to reinvent the wheel. Given that conclusion, I'm going to move 
over to R-devel and try to convince them to add this feature to R....


Vincent Carey 525-2265 wrote:
> This is an important topic.  I believe that the building/checking
> process is a key source of value added by the Bioc project for developers.
> A worthwhile thought experiment: What would be done if we had unlimited
> resources?  It seems to me that a primary resource that a developer
> lacks access to is the range of platforms -- hardware, OS, compilers --
> that we want users to be able to work with reliably.  Thus a very
> high priority for the build/check system is coverage of the main
> varieties of "system" that users are likely to use Bioconductor on.
> The devel branch is very important because it indicates how ongoing
> changes to R affect performance/accuracy/interactions of package code.  Most
> developers aren't going to be updating R and all other packages approximately
> daily.  Thus, without the devel build system, many developers would
> find themselves working hard when a new R release became imminent, to
> port abruptly to the new release.  The devel build system allows this
> to occur somewhat more smoothly, and affords the possibility of feedback
> to R core when tentative changes to R are problematic.
> I recognize that the points just made are well-known, and these remarks
> are not made defensively.  Instead I am trying to come up with some
> a priori limits to testing requirements falling to bioconductor, as
> opposed to requirements that lie uniquely with the developer.  So the
> first two priorities are, briefly:
> 1) Cover the platforms
> 2) Track performance relative to evolving R
> Now we know full well that our resources require that package testing
> be limited to around five minutes.  Is this in itself a value or an
> obstacle to ensuring project/package reliability?
> My sense is that this constraint might be a value -- I understand that
> a very multifaceted package may have many essential tests that can finish
> rapidly but the sum of testing times exceeds our limits.  Perhaps that
> package should be broken up... Perhaps it should get an exception...
> I don't know.  Other things being equal, I think it is good for the software
> that there be cases that are legitimate tests that run quickly.  It means
> users can demonstrate the functionality in short order, that the tests
> can be varied and examined without long delay, and that, probably, we
> have capacity to do more tests of different facets of the package.
>>From the project perspective, I feel that the tests we need to be
> concerned about most involve tests that would indicate problems with
> respect to priorities 1) and 2).  Portability problems, or dependencies
> on ephemeral features of R, might only crop up with certain very long
> tests ... but I think that would be exceptional.  Thus the deep tests
> should be done "at home" and the light ones left for the project
> system.
> Finally, the complexity of the project test/build system has to be
> kept very manageable -- we have {release, devel} X platform X {software,
> experiment, annotation} and introducing a short/long testing stream
> may be feasible but may not pay off.  The point is that even if we did
> have a lot more resources I am not sure it would be sound to allow
> indefinite test return times.
> I am open to correction or criticism on any point made above.  I am
> trying to articulate some points about testing in the project that
> are probably quite superficial from the perspective of serious software
> development and engineering -- yet the breadth of testing
> accomplished and the necessity of release/devel branches is not very
> widely appreciated among some of my contacts in other domains ...
> so I have taken this opportunity to articulate these views to the devel
> group.
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