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

[Jisca Huisman]

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 using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel