On 25 August 2023 at 15:37, Uwe Ligges wrote:
|
|
| On 23.08.2023 16:00, Scott Ritchie wrote:
| > Hi Uwe,
| >
| > I agree and have also been burnt myself by programs occupying the
| > maximum number of cores available.
| >
| > My understanding is that in the absence of explicit
roject.org>
mailto:r-package-devel@r-project.org>>
> Subject: Re: [R-pkg-devel] Trouble with long-running tests on
CRAN debian server
>
> Thanks Dirk and Ivan,
>
> I took a slightly different work-around of forcing the number of
that a lot of code to
>>>> read + maintain?
>>>> Also, it seems like unnecessary computational overhead.
>>>> From a software design point of view, it might be nicer to set that in
>>>> the examples + tests.
>>>>
>>>> Reg
, it might be nicer to set that in the
examples + tests.
Regards,
Berry
From: R-package-devel on behalf of Scott
Ritchie
Sent: Monday, August 21, 2023 19:23
To: Dirk Eddelbuettel
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Trouble with long-running
software design point of view, it might be nicer to set that in
> the examples + tests.
> >
> > Regards,
> > Berry
> >
> >
> > From: R-package-devel on behalf
> of Scott Ritchie
> > Sent: Monday, August 21, 2023 19:23
> > To: Dirk
; examples + tests.
>>
>> Regards,
>> Berry
>>
>>
>> From: R-package-devel on behalf of
>> Scott Ritchie
>> Sent: Monday, August 21, 2023 19:23
>> To: Dirk Eddelbuettel
>> Cc: r-package-devel@r-project
21, 2023 19:23
To: Dirk Eddelbuettel
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server
Thanks Dirk and Ivan,
I took a slightly different work-around of forcing the number of threads to
1 when running functions of the test dataset
_
From: R-package-devel on behalf of
Scott Ritchie
Sent: Monday, August 21, 2023 19:23
To: Dirk Eddelbuettel
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server
Thanks Dirk and Ivan,
I took a slightly different work-around of f
Thanks Dirk and Ivan,
I took a slightly different work-around of forcing the number of threads to
1 when running functions of the test dataset in the package, by adding the
following to each user facing function:
```
# Check if running on package test_data, and if so, force data.table to
be
On 21 August 2023 at 16:05, Ivan Krylov wrote:
| Dirk is probably right that it's a good idea to have OMP_THREAD_LIMIT=2
| set on the CRAN check machine. Either that, or place the responsibility
| on data.table for setting the right number of threads by default. But
| that's a policy question:
On Mon, 21 Aug 2023 13:28:54 +0100
Scott Ritchie wrote:
> Examples with CPU time > 2.5 times elapsed time
> user system elapsed ratio
> remove_technical_variation 2.603 0.0270.94 2.798
In this context, "user" means the time spent executing userspace code
(as
On 21/08/2023 14:34, Dirk Eddelbuettel wrote:
On 21 August 2023 at 15:16, Ivan Krylov wrote:
| On Mon, 21 Aug 2023 12:02:55 +0100
| Scott Ritchie wrote:
|
| > remotes::install_github("sritchie73/ukbnmr")
| > library(ukbnmr)
| > system.time({ remove_technical_variation(test_data) })
|
|
On 21 August 2023 at 15:16, Ivan Krylov wrote:
| On Mon, 21 Aug 2023 12:02:55 +0100
| Scott Ritchie 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
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 0.0270.94 2.798
This doesn't appear to be related to data.table threads,
On Mon, 21 Aug 2023 12:02:55 +0100
Scott Ritchie 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
Dear all,
I'm currently having issues submitting an update to the ukbnmr package to
CRAN as the checks on their debian server are generating a NOTE due to long
running tests.
The offending test code is much faster on my own machine, and on all other
CRAN servers (running in < 1 second), and I
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