Re: [R-pkg-devel] NOTE checking for detritus in the temp directory on windows
Hi, Thanks a lot Henrik for your detailed response, the problem was the one you suspected a "plan(mutlisession)" that was not correctly closed. And following your advice I was able to reproduce it on winbuilder. So thanks again for your help! Best regards, Etienne Etienne Côme, @comeetie Chargé de Recherche Université Gustave Eiffel GRETTIA/COSYS Tel : 01 81 66 87 18 Web : http://www.comeetie.fr - Mail original - De: "Henrik Bengtsson" À: "etienne come" Cc: "r-package-devel" Envoyé: Vendredi 30 Septembre 2022 17:19:03 Objet: Re: [R-pkg-devel] NOTE checking for detritus in the temp directory on windows Hi. > * checking for detritus in the temp directory ... NOTE > Found the following files/directories: > 'Rscript306c1f1adf1' 'Rscript3fb41f1adf1' Whenever seeing detritus files with name Rscript like these, it's a strong suggestion that parallel workers on MS Windows are involved. More precisely, each of them is from a separate PSOCK cluster node worker typically launched by parallel::makeCluster(). When such workers are launched in example code, unit tests, or vignettes those files are created by R itself when running on MS Windows. If the workers are not properly shutdown (e.g. forgetting to call parallel::stopCluster()), those files are left behind, and 'R CMD check' will detect them. Now, from experience, but neither fully investigated not understood yet, it *might* be that even if one calls parallel::stopCluster() at the end of examples, unit tests, or vignettes, it might be that there is still a race condition where the parallel workers are still in the process of shutting down when 'R CMD check' is checking for detritus files. If that is the case, then it might be sporadic and tricky to reproduce this problem. This has happened to me exactly once. I'm saying this, only in case you're struggle to reproduce it, but my guess is that this is *not* the case here. Please see below for options how to reproduce. Now, I see you're using 'future' for parallelization. Because of this, I suspect you use plan(multisession), which launches parallel PSOCK workers like parallel::makeCluster(). To shut down those workers at the end, call plan(sequential). My guess is that this is your problem. Before you do that, I would make sure you can reproduce the problem first - see below. > I did not manage to reproduce it with Rhub and github action. 1. Looking at your https://github.com/comeetie/greed/blob/master/.github/workflows/R-CMD-check.yaml, I see you're not checking with **R-devel** on MS Windows. I suggest you add that and too see if you can reproduce it there. You could also add an explicit `env: _R_CHECK_THINGS_IN_TEMP_DIR_: true` just in case (but I'd guess --as-cran does this). 2. Similarly, did you make sure to test with R-devel on MS Windows on R-hub? 3. Did you try with R-devel on the win-builder service? For your future needs (pun not intended), I would make sure you can reproduce the problem before trying to fix it. Hope this helps, Henrik On Fri, Sep 30, 2022 at 12:14 AM wrote: > > Dear all, > > I'm getting the following Note for CRAN pre-tests (for package greed > https://github.com/comeetie/greed) : > > * checking for detritus in the temp directory ... NOTE > Found the following files/directories: > 'Rscript306c1f1adf1' 'Rscript3fb41f1adf1' > > this note only appears on windows : > > * using R Under development (unstable) (2022-09-26 r82921 ucrt) > * using platform: x86_64-w64-mingw32 (64-bit) > > The full pretest logs are located at > https://win-builder.r-project.org/incoming_pretest/greed_0.6.1_20220927_163632/Windows/00check.log > > I did not manage to reproduce it with Rhub and github action. > > I've seen other questions on the mailing list about "detritus" but the root > causes seems to be different in my case since i did not open a navigator and > i did not create > files or folders in my tests or vignettes. Any hint on how to solve this note > will be welcome. > > Thanks a lot > > Etienne > > > Etienne Côme, @comeetie > Chargé de Recherche > Université Gustave Eiffel > GRETTIA/COSYS > Tel : 01 81 66 87 18 > Web : http://www.comeetie.fr > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE checking for detritus in the temp directory on windows
Hi. > * checking for detritus in the temp directory ... NOTE > Found the following files/directories: > 'Rscript306c1f1adf1' 'Rscript3fb41f1adf1' Whenever seeing detritus files with name Rscript like these, it's a strong suggestion that parallel workers on MS Windows are involved. More precisely, each of them is from a separate PSOCK cluster node worker typically launched by parallel::makeCluster(). When such workers are launched in example code, unit tests, or vignettes those files are created by R itself when running on MS Windows. If the workers are not properly shutdown (e.g. forgetting to call parallel::stopCluster()), those files are left behind, and 'R CMD check' will detect them. Now, from experience, but neither fully investigated not understood yet, it *might* be that even if one calls parallel::stopCluster() at the end of examples, unit tests, or vignettes, it might be that there is still a race condition where the parallel workers are still in the process of shutting down when 'R CMD check' is checking for detritus files. If that is the case, then it might be sporadic and tricky to reproduce this problem. This has happened to me exactly once. I'm saying this, only in case you're struggle to reproduce it, but my guess is that this is *not* the case here. Please see below for options how to reproduce. Now, I see you're using 'future' for parallelization. Because of this, I suspect you use plan(multisession), which launches parallel PSOCK workers like parallel::makeCluster(). To shut down those workers at the end, call plan(sequential). My guess is that this is your problem. Before you do that, I would make sure you can reproduce the problem first - see below. > I did not manage to reproduce it with Rhub and github action. 1. Looking at your https://github.com/comeetie/greed/blob/master/.github/workflows/R-CMD-check.yaml, I see you're not checking with **R-devel** on MS Windows. I suggest you add that and too see if you can reproduce it there. You could also add an explicit `env: _R_CHECK_THINGS_IN_TEMP_DIR_: true` just in case (but I'd guess --as-cran does this). 2. Similarly, did you make sure to test with R-devel on MS Windows on R-hub? 3. Did you try with R-devel on the win-builder service? For your future needs (pun not intended), I would make sure you can reproduce the problem before trying to fix it. Hope this helps, Henrik On Fri, Sep 30, 2022 at 12:14 AM wrote: > > Dear all, > > I'm getting the following Note for CRAN pre-tests (for package greed > https://github.com/comeetie/greed) : > > * checking for detritus in the temp directory ... NOTE > Found the following files/directories: > 'Rscript306c1f1adf1' 'Rscript3fb41f1adf1' > > this note only appears on windows : > > * using R Under development (unstable) (2022-09-26 r82921 ucrt) > * using platform: x86_64-w64-mingw32 (64-bit) > > The full pretest logs are located at > https://win-builder.r-project.org/incoming_pretest/greed_0.6.1_20220927_163632/Windows/00check.log > > I did not manage to reproduce it with Rhub and github action. > > I've seen other questions on the mailing list about "detritus" but the root > causes seems to be different in my case since i did not open a navigator and > i did not create > files or folders in my tests or vignettes. Any hint on how to solve this note > will be welcome. > > Thanks a lot > > Etienne > > > Etienne Côme, @comeetie > Chargé de Recherche > Université Gustave Eiffel > GRETTIA/COSYS > Tel : 01 81 66 87 18 > Web : http://www.comeetie.fr > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] NOTE checking for detritus in the temp directory on windows
Dear all, I'm getting the following Note for CRAN pre-tests (for package greed https://github.com/comeetie/greed) : * checking for detritus in the temp directory ... NOTE Found the following files/directories: 'Rscript306c1f1adf1' 'Rscript3fb41f1adf1' this note only appears on windows : * using R Under development (unstable) (2022-09-26 r82921 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) The full pretest logs are located at https://win-builder.r-project.org/incoming_pretest/greed_0.6.1_20220927_163632/Windows/00check.log I did not manage to reproduce it with Rhub and github action. I've seen other questions on the mailing list about "detritus" but the root causes seems to be different in my case since i did not open a navigator and i did not create files or folders in my tests or vignettes. Any hint on how to solve this note will be welcome. Thanks a lot Etienne Etienne Côme, @comeetie Chargé de Recherche Université Gustave Eiffel GRETTIA/COSYS Tel : 01 81 66 87 18 Web : http://www.comeetie.fr [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel