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
https://bioconductor.org/checkResults/3.13/bioc-LATEST/MungeSumstats/nebbiolo1-checksrc.html
and here
https://bioconductor.org/checkResults/3.14/bioc-LATEST/MungeSumstats/nebbiolo2-checksrc.html
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.
Cheers,
H.
Thanks,
Alan.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
