[Bioc-devel] Dev check runtime on all machines

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Wed Oct 13 22:11:48 CEST 2021

Hi Alan,

On 13/10/2021 11:22, alan murphy wrote:
> Hi all,
> I'm the developer of the MungeSumstats package which is currently timing out on the nightly builds for windows (riesling1) but doesn't have any errors: https://bioconductor.org/checkResults/3.14/bioc-LATEST/MungeSumstats/riesling1-checksrc.html.
> My question is whether there is a reason the builds took a particularly long time yesterday?

Running the tests in MungeSumstats takes 228.551 sec. on nebbiolo1 
(Linux release builder) and 659.874 sec. on nebbiolo2 (Linux devel 
builder) so it looks like you added a lot of unit tests to the devel 
version of your package. BTW those times are displayed here


and here


It's a very good thing that you add so many tests to your package. 
Remember however that on Windows we run 'R CMD check' with the 
--force-multiarch option to force all the examples and tests to run 
twice: once in 32-bit mode and once in 64-bit mode. This probably 
explains why you see the TIMEOUT on Windows and not on the other builders.

> For example, the MAC (merida1) check ran in 21 minutes but running devtools::check() locally after removing all cached items runs in 12.5 minutes. Secondly, is there a way to check how long the unit tests took to run on each machine? It doesn't seem to be available in the raw or summarised build reports.
> I ask because if the checks should generally run quicker I won't make any changes to my package to speed up the check. Otherwise, I will likely remove some unit tests which I believe account for a decent part of the runtime.

One way to deal with this is to disable the tests on 32-bit Windows. 
This platform will go away soon anyways so there's not much value in 
running the tests for it anymore.

Another option for you, especially if you want to be able to keep adding 
tests to your package, is to add "long tests" to your package and to 
subscribe to our Long Tests builds. See here 
https://bioconductor.org/checkResults/3.14/bioc-longtests-LATEST/ for 
more info.

Hope this helps.


> Thanks,
> Alan.
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

More information about the Bioc-devel mailing list