R devel - Jan 2023 - rhub vs. CRAN fedora-*-devel, using armadillo & slapack

Le 10/01/2023 ? 11:37, Serguei Sokol a ?crit?:
> Le 10/01/2023 ? 10:44, RICHET Yann a ?crit?:
>> Dear R-devel people,
>>
>> We are working to submit a package which is mainly a binding over a 
>> C++ lib (https://github.com/libKriging) using armadillo.
>> It is _not_ a standard RcppArmadillo package, because we also had to 
>> provide a python binding... so there is a huge layer of cmake & 
>> scripting to make it work with a standard armadillo (but using same 
>> version that RcppArmadillo).
>> It seems now working with almost all CRAN targets, but a problem 
>> remains with fedora (clang & gcc) devel.
>>
>> Our issue is that the rhub docker is not well sync with the CRAN 
>> fedora-clang-devel config:
>> - failing on CRAN (without clear reason): 
>>
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/rlibkriging-00check.html
> I see? 2 candidates for? reasons of failing on CRAN:
> ?1. test time is 30 min while 15 min are allowed;
> ?2. your code try to get 30 threads
Oops, it was 10 threads not 30 but it does not change the nature of a 
possible issue.
> while CRAN limits them to 2;
>
> Try to make your tests shorter ( < 15 min) on 2 threads. May be it 
> will help.
>
> Best,
> Serguei.
>
>> - passing on rhub: 
>>
https://builder.r-hub.io/status/rlibkriging_0.7-3.tar.gz-20f7dc7562726497af7c678ab41f4dea
>>
>> So we cannot investigate and fix the problem.
>>
>> Note that we did quite strange things with the fedora platforms: 
>> include explicitely slapack to provide simple precision for our 
>> (vanilla) armadillo...
>>
>> Do you have any idea, or even known problem in mind, that could be 
>> related to this ?
>>
>> Best regards,
>>
>> -- 
>> Dr. Yann Richet
>> Institute for Radiological Protection and Nuclear Safety 
>> (https://www.irsn.fr),
>> ?? Department of Characterization of Natural Unexpected Events and
Sites
>> Office?: +33 1 58 35 88 84
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Serguei Sokol
Ingenieur de recherche INRAE

Cellule Math?matiques
TBI, INSA/INRAE UMR 792, INSA/CNRS UMR 5504
135 Avenue de Rangueil
31077 Toulouse Cedex 04

tel: +33 5 61 55 98 49
email: sokol at insa-toulouse.fr
http://www.toulouse-biotechnology-institute.fr/en/technology_platforms/mathematics-cell.html

Thank you for your answer.
In facts, 10 threads are asked by armadillo for some LinAlg, which backs to two
threads as warned. But I cannot imagine this costs so much time just for that...

A deeper analysis of time spent seems to point that a large time was mainly
spent on testthat and Rcpp dependencies compilation... But other recent packages
depending on these also are not spending so much time.

CRAN team, as I failed to reproduce the issue with rhub dockers, 
- is there any reason that could explain that fedora-*-devel is so slow for this
package or compilation of Rcpp/testthat ?
- is our slapack a possible source of... anything ?
- are we the only package which embeds "standard armadillo" and tries
to deal with simple precision lapack issues on fedora ?
- is there any chance that I can get a deeper log of what happened ?

Best regards,

Yann

-----Message d'origine-----
De?: Serguei Sokol <sokol at insa-toulouse.fr> 
Envoy??: mardi 10 janvier 2023 11:41
??: RICHET Yann <yann.richet at irsn.fr>; R-devel at r-project.org
Cc?: Pascal Hav? <pascal at haveneer.com>
Objet?: Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

Le 10/01/2023 ? 11:37, Serguei Sokol a ?crit?:
> Le 10/01/2023 ? 10:44, RICHET Yann a ?crit?:
>> Dear R-devel people,
>>
>> We are working to submit a package which is mainly a binding over a
>> C++ lib (https://github.com/libKriging) using armadillo.
>> It is _not_ a standard RcppArmadillo package, because we also had to 
>> provide a python binding... so there is a huge layer of cmake & 
>> scripting to make it work with a standard armadillo (but using same 
>> version that RcppArmadillo).
>> It seems now working with almost all CRAN targets, but a problem 
>> remains with fedora (clang & gcc) devel.
>>
>> Our issue is that the rhub docker is not well sync with the CRAN 
>> fedora-clang-devel config:
>> - failing on CRAN (without clear reason): 
>> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-c
>> lang/rlibkriging-00check.html
> I see? 2 candidates for? reasons of failing on CRAN:
> ?1. test time is 30 min while 15 min are allowed;
> ?2. your code try to get 30 threads
Oops, it was 10 threads not 30 but it does not change the nature of a possible
issue.
> while CRAN limits them to 2;
>
> Try to make your tests shorter ( < 15 min) on 2 threads. May be it 
> will help.
>
> Best,
> Serguei.
>
>> - passing on rhub: 
>> https://builder.r-hub.io/status/rlibkriging_0.7-3.tar.gz-20f7dc756272
>> 6497af7c678ab41f4dea
>>
>> So we cannot investigate and fix the problem.
>>
>> Note that we did quite strange things with the fedora platforms: 
>> include explicitely slapack to provide simple precision for our
>> (vanilla) armadillo...
>>
>> Do you have any idea, or even known problem in mind, that could be 
>> related to this ?
>>
>> Best regards,
>>
>> --
>> Dr. Yann Richet
>> Institute for Radiological Protection and Nuclear Safety 
>> (https://www.irsn.fr),
>> ?? Department of Characterization of Natural Unexpected Events and 
>> Sites Office?: +33 1 58 35 88 84
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

--
Serguei Sokol
Ingenieur de recherche INRAE

Cellule Math?matiques
TBI, INSA/INRAE UMR 792, INSA/CNRS UMR 5504
135 Avenue de Rangueil
31077 Toulouse Cedex 04

tel: +33 5 61 55 98 49
email: sokol at insa-toulouse.fr
http://www.toulouse-biotechnology-institute.fr/en/technology_platforms/mathematics-cell.html