[R-pkg-devel] Vignette build issue on Debian platform

[Graeme Hickey]

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]]