Thank you, Jisca. I learned something new. Unfortunately the NOTE was not being triggered by this, but rather somehow the package was using OpenMP. I found the trick was to throttle the number of OpenMP threads courtesy of Dirk Edubuettel's post here: https://dirk.eddelbuettel.com/blog/2023/10/31/.
On Tue, 14 Jan 2025 at 16:34, Jisca Huisman <jisca.huis...@gmail.com> wrote: > Hi Graeme, > > > There is only one function in my package that uses multiple cores: > > bootSE(). However, this function is not called in any of my vignettes > > because it is computationally expensive. The Rmd code has `eval = FALSE` > > options for all of these cases. Therefore, I am at a loss as to why these > > vignettes would be using more than 2 cores or what is causing this, or > why > > it only impacts the CRAN CMD check Debian system. > > CRAN has changed its settings when compiling the vignette, and now > *does* run everything in chunks with `eval = FALSE`. The solution is to > also add `purl=FALSE` to each chunk that should not be run. > > If you dig through the mailing list archive you should be able to find > further details on the why and how of this, or someone else might remember. > > Best, > > Jisca > > > > On Tue, 14/01/2025 08:08, Graeme Hickey wrote: > > Dear all, > > > > > > I recently made some minor updates to the joineRML R package to squash > some > > CRAN CMD check NOTEs that have emerged over the past couple of years. > After > > resubmitting to CRAN, a new NOTE appeared on the Debian platform only: > > > > > >> package joineRML_0.4.7.tar.gz does not pass the incoming checks > > automatically, please see the following pre-tests (additional issue > checks): > > > >> Windows: < > > > https://win-builder.r-project.org/incoming_pretest/joineRML_0.4.7_20250114_073418/Windows/00check.log > >> Status: OK > >> Debian: < > > > https://win-builder.r-project.org/incoming_pretest/joineRML_0.4.7_20250114_073418/Debian/00check.log > >> Status: 1 NOTE > > > > The NOTE in particular is: > > > > > >> * checking re-building of vignette outputs ... [116s/30s] NOTE > >> Re-building vignettes had CPU time 3.9 times elapsed time > > > > I emailed Uwe Ligges and got a reply: > > > > > >> We see > >> Flavor: r-devel-linux-x86_64-debian-gcc > >> Check: re-building of vignette outputs, Result: NOTE > >> Re-building vignettes had CPU time 3.9 times elapsed time > > > >> which suggests you are using more than 2 cores which is not permitted by > > default. > > > > > > There is only one function in my package that uses multiple cores: > > bootSE(). However, this function is not called in any of my vignettes > > because it is computationally expensive. The Rmd code has `eval = FALSE` > > options for all of these cases. Therefore, I am at a loss as to why these > > vignettes would be using more than 2 cores or what is causing this, or > why > > it only impacts the CRAN CMD check Debian system. > > > > > > I noticed this has been a common reported issue (e.g., > > https://github.com/Rdatatable/data.table/issues/5658), but mainly for > those > > using data.table or openMP; I use neither. The same issue was showing for > > some examples also, which I dealt with by wrapping in \dontrun{} — not > > ideal, but seemed quickest way to avoid. > > > > > > I have tried many things to fix this: > > > > 1. Modifying the vignettes to make faster > > 2. Adding various combinations of Sys.setenv("OMP_THREAD_LIMIT" = 1), > > Sys.setenv("OMP_NUM_THREADS" = 1), options(Ncpus = 1), options(cores > = 2) > > to the Rmd vignettes > > 3. Checked the package builds using r-lib/actions (GitHub actions) > and > > r-hub Debian platform — I cannot reproduce this CRAN error > > > > > > CRAN will not accept the update to my package until this NOTE is > squashed. > > If anyone is able to provide a recommendation on what I might do, I would > > appreciate it. > > > > > > Kind regards, > > > > > > Graeme Hickey > > > > [[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 > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
