[R-pkg-devel] Trouble with long-running tests on CRAN debian server

[Scott Ritchie]

Hi Ivan,

Here is the NOTE generated by CRAN:

* checking examples ... [5s/2s] NOTE
Examples with CPU time > 2.5 times elapsed time
                            user system elapsed ratio
remove_technical_variation 2.603  0.027    0.94 2.798

This doesn't appear to be related to data.table threads, here is what
I see after explicitly setting setDTthreads(1)

On my own machine (OSX Monterey, arm64 M1 processor):

> system.time({ remove_technical_variation(test_data) })
   user  system elapsed
  0.460   0.004   0.466

And on my University's cluster (RHEL 7, intel xeon platinum 8276 CPU @ 2.2 GHz):

> system.time({ remove_technical_variation(test_data) })
   user  system elapsed
  1.108   0.020   1.130

Runtimes are similar on these two machines when using an older version
of ukbnmr that has a 5x- larger test dataset (50 rows instead of 10
rows).

Best,

Scott


On Mon, 21 Aug 2023 at 13:16, Ivan Krylov <krylov.r00t using gmail.com> wrote:

> On Mon, 21 Aug 2023 12:02:55 +0100
> Scott Ritchie <sritchie73 using gmail.com> wrote:
>
> > remotes::install_github("sritchie73/ukbnmr")
> > library(ukbnmr)
> > system.time({ remove_technical_variation(test_data) })
>
> data.tables, you say? Can you show us the NOTE message you're getting?
> It could be that your example takes too much CPU time (as opposed to
> "real", "wallclock" time) due to running too many threads started by
> data.table.
>
> It's not obvious why data.table would start too many threads (it's
> supposed to honour the limits that CRAN expresses in environment
> variables), but at least it should be easy to check and discount.
>
> --
> Best regards,
> Ivan
>

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