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

[Graeme Hickey]

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.huisman using 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]]
> >
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