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

Wolfgang Huber huber at ebi.ac.uk
Tue Jun 10 22:33:17 CEST 2008

Just to clarify... vignettes are being used in Bioconductor for two 
purposes, documentation and checking. These often overlap, but of course 
don't always have to. In the case described below, they do, and the 
solution described is geared towards such cases.

Wolfgang Huber a écrit 10/06/2008 21:27:
> Dear Kevin,
>> I also understand the need for the time limits, and agree with their 
>> rationale. But building ("R CMD build" or "R CMD build --binary") for 
>> the package I'm putting together is pretty fast. The part that takes 
>> time is checking, largely because I am running regression tests on 
>> several different honest-to-god real data sets. And I'm doing the 
>> testing with at least three different statistical models to fit the 
>> data (since we don't claim to know which one will ultimately turn out 
>> to be the best). Now, I could game the system by breaking everything 
>> into 3 different sub-packages, where each test could probably be 
>> completed within five minutes. However, that seems like a rather 
>> artificial approach to the problem.  I guess what I'd really like is 
>> two different levels of testing. In addition to the time-consuming 
>> tests, my package also has scripts that do basic tests to make sure 
>> that the code behaves (as) sensibly (as possible) even when the user 
>> hands it the wrong kind of inputs. It would be nice to have a system 
>> that allowed these "easy but important interface tests" to run 
>> routinely while keeping the "time consuming core algorithm 
>> development" tests around for when you are testing out more radical 
>> changes.
> I think I had similar issues with the vsn and tilingArray package. They 
> contain tests of their functionalities in their vignettes that take 
> hours or days, and >10GB of RAM in the tilingArray case. Like you, I 
> feel that these are necessary to properly test the packages, but there 
> is no way the build system in Seattle should do this every night.
> So the vignettes sit in the inst/scripts directory, and I (or anyone) 
> can invoke them manually when they feel the urge. You might be 
> interested in the "Makefile" in inst/doc that makes sure that the PDFs 
> from these vignettes are still visible to package users like "normal" 
> vignettes.

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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