[R-pkg-devel] Two problems with fda

[Avraham Adler]

Hello, Spencer.

What you may want to try is updating the R-CMD-Check workflow. Your
YAML is from the early days of github actions [1]. I just updated it
for the lamW package to ensure github is using Rtools42. There is a
version 2 of both setupR and pandoc; it may be buried there. Please
see [2] which I know successfully completes [3]. At worst, it
eliminates the outdated YAML from being a cause. As for the second
issue, I believe it means line 325 column 22 of the tex file created
by rhe Rd file, which may not conform to the Rd file itself, which may
have different line lengths. I didn't see any unclosed \code{}
elements; the only place where you wrap it is in lines 312-315.

Hope that helps,

Avi

[1] https://github.com/JamesRamsay5/fda/blob/master/.github/workflows/R-CMD-check.yaml
[2] https://github.com/aadler/lamW/blob/master/.github/workflows/R-CMD-check.yaml
[3] https://github.com/aadler/lamW/actions/runs/2216065520


On Mon, Apr 25, 2022 at 8:07 PM Spencer Graves
<spencer.graves using effectivedefense.org> wrote:
>
> Hello, All:
>
>
>           Jim Ramsay and I have two problems with
> "https://github.com/JamesRamsay5/fda/":
>
>
>                     1. GitHub action reports, <<'"pdflatex"' not found>> with
> vignettes.  We have two problems with this:  (1.1) We don't know how to
> report them to the "GitHub action" maintainer(s).  (1.2) We don't know
> what in the vignettes require pdflatex, so we cannot easily remove that.
>
>
>                     2.  A CRAN submission now triggers a "win-builder" pretest on
> Debian, which complains, "fRegress.Rd:325:22: Warning: nested emphasis
> <code>".[1]  We have three problems with this:  (2.1) We cannot find any
> "nested emphasis" to fix in this.  (2.2) We don't know what the numbers
> "325:22" mean.  (2.3) We don't know how to run this win-builder on
> Debian other than to submit a new version to CRAN.  If we could run this
> Debian win-builder without submitting a version to CRAN, we could do a
> binary search submitting "fRegress.Rd" that we would not want to share
> with users but would still pass "R CMD build / check" for us locally
> until we isolated the problem.
>
>
>           Suggestions?
>           Thanks,
>           Spencer Graves
>
>
> [1]
> https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/Debian/00check.log
>
>
> -------- Forwarded Message --------
> Subject:        Fwd: [CRAN-pretest-archived] CRAN Submission fda 6.0.2
> Date:   Fri, 22 Apr 2022 18:13:56 +0000
> From:   James Owen Ramsay, Dr. <james.ramsay using mcgill.ca>
> To:     Spencer Graves <spencer.graves using effectivedefense.org>
>
>
>
> Rejection email:
>
> Jim Ramsay
> james.ramsay using mcgill.ca <mailto:james.ramsay using mcgill.ca>
>
>
>
> > Begin forwarded message:
> >
> > *From: *ligges using statistik.tu-dortmund.de
> > <mailto:ligges using statistik.tu-dortmund.de>
> > *Subject: **[CRAN-pretest-archived] CRAN Submission fda 6.0.2*
> > *Date: *April 22, 2022 at 1:01:55 PM EDT
> > *To: *ramsay using psych.mcgill.ca <mailto:ramsay using psych.mcgill.ca>
> > *Cc: *CRAN-submissions using R-project.org
> > <mailto:CRAN-submissions using R-project.org>
> > *Reply-To: *CRAN-submissions using R-project.org
> > <mailto:CRAN-submissions using R-project.org>
> >
> > Dear maintainer,
> >
> > package fda_6.0.2.tar.gz does not pass the incoming checks
> > automatically, please see the following pre-tests:
> > Windows:
> > <https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/Windows/00check.log
> > <https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/Windows/00check.log>>
> > Status: OK
> > Debian:
> > <https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/Debian/00check.log
> > <https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/Debian/00check.log>>
> > Status: 1 NOTE
> >
> > Last released version's CRAN status: OK: 12
> > See: <https://CRAN.R-project.org/web/checks/check_results_fda.html
> > <https://CRAN.R-project.org/web/checks/check_results_fda.html>>
> >
> > CRAN Web: <https://cran.r-project.org/package=fda
> > <https://cran.r-project.org/package=fda>>
> >
> > Please fix all problems and resubmit a fixed version via the webform.
> > If you are not sure how to fix the problems shown, please ask for help
> > on the R-package-devel mailing list:
> > <https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > <https://stat.ethz.ch/mailman/listinfo/r-package-devel>>
> > If you are fairly certain the rejection is a false positive, please
> > reply-all to this message and explain.
> >
> > More details are given in the directory:
> > <https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/
> > <https://win-builder.r-project.org/incoming_pretest/fda_6.0.2_20220422_184836/>>
> > The files will be removed after roughly 7 days.
> >
> > *** Strong rev. depends ***: adass anacor BayesOrdDesign CausalKinetiX
> > CCA cfda clustEff CollocInfer Compack conformalInference.fd CSTE
> > ctmcmove cyphid dfrr dynr EBCHS Ecfun ExtremalDep FADPclust fda.usc
> > fdaACF fdaMocca fdANOVA fdatest FDRreg flars freqdom.fda ftsa
> > funcharts FuncNN funFEM funHDDC funLBM geofd GPFDA iWISA KFPCA LocKer
> > logitFD mar1s mixedClust MRmediation mxnorm NITPicker pcdpca pCODE
> > pencopulaCond pendensity penDvine PerFit pfica puls PupillometryR
> > quantreg.nonpar refund Rfssa robCompositions Rsfar sasfunclust SCCS
> > sde sft slasso SLFPCA srp stfit switchnpreg T4cluster TestGardener
> > trackeR vows warpMix
> >
> > Best regards,
> > CRAN teams' auto-check service
> > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
> > Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
> >  Maintainer: 'J. O. Ramsay <ramsay using psych.mcgill.ca
> > <mailto:ramsay using psych.mcgill.ca>>'
> >
> > Flavor: r-devel-linux-x86_64-debian-gcc
> > Check: HTML version of manual, Result: NOTE
> >  Found the following problems:
> >  fRegress.Rd:325:22: Warning: nested emphasis <code>
>
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