[Bioc-devel] Methods to speed up R CMD Check

[Murphy, Alan E]

Hi all,

I am working on the development of [EWCE](https://github.com/NathanSkene/EWCE) but have hit an issue with R CMD check's runtime. I have been informed this test needs to be completed in 15 minutes but mine is currently running in ~24 minutes and I am looking for methods to speed this up. The main culprits for the runtime issue are:

checking examples (5m 49.8s)
Running �testthat.R� [308s/469s] (7m 49.1s)
checking for unstated dependencies in vignettes (7m 49.4s)
checking re-building of vignette outputs (5m 12s)

With the exception of using smaller datasets which I will consider myself, is there known ways of speeding these up? EWCE derives data from an Experimenthub package [ewceData](https://github.com/neurogenomics/ewceData) for its examples, tests and vignette. This is run repeatedly and I have noted this takes a significant amount of time to load a dataset. Is there anyway of caching the datasets for all the checks or more generally of speeding this up?

I have heard of the use of [long tests](http://bioconductor.org/developers/how-to/long-tests/) which aren't run daily by Bioconductor but are these still checked in R CMD Check? Is there any other way to exclude my tests from the R CMD Check given they aren't a necessity from Bioconductor?

Does checking for unstated dependencies in vignettes have a long runtime based on the number of package dependencies? If I just export specific functions from packages will this check time reduce?

Lastly, is there any way to get an exception of the 15 minute maximum? I may be ill-informed but is the max time for packages on Bioconductor's daily check 40 minutes which my code in its current state would complete by.

Kind regards,
Alan.


	[[alternative HTML version deleted]]