A simple fix might be to redefine findFn in the global environment of the
vignette, have it explicitly call sos::findFn, and return a result
sanitized for LaTeX output. According to this:
https://stackoverflow.com/questions/32865384/function-to-sanitize-strings-for-latex-compilation
it looks like there are a couple of options for that.
On Mon, May 22, 2023 at 1:39 PM Spencer Graves <
spencer.gra...@effectivedefense.org> wrote:
> Hi, Uwe et al.:
>
>
> The sos vignette sos.Rnw now fails on GitHub, complaining of a
> LaTeX
> error in "{\tt pspline_ checker}". I don't find it in the code for
> sos.Rnw. It may be triggered by a response to an internet search that's
> different from before.
>
>
> https://github.com/sbgraves237/sos
>
>
> Uwe suggests I postprocess output with gsub("_", "\\\\_",
> output).
> It's not clear to me where I should apply this. I am not eager to
> change the code in the package, because it could break something else
> that's currently working.
>
>
> Suggestions?
> Thanks
> Spencer Graves
>
>
> On 5/16/23 7:41 AM, Uwe Ligges wrote:
> >
> >
> > On 16.05.2023 14:02, Spencer Graves wrote:
> >>
> >>
> >> On 5/16/23 6:06 AM, Uwe Ligges wrote:
> >>>
> >>>
> >>> On 16.05.2023 01:46, Spencer Graves wrote:
> >>>> Hello, All:
> >>>>
> >>>>
> >>>> The sos package is failing some CRAN checks, complaining:[1]
> >>>>
> >>>>
> >>>> LaTeX errors:
> >>>> ! Missing $ inserted.
> >>>> <inserted text>
> >>>> $
> >>>> l.303 {\tt pspline_
> >>>> checker} in the
> >>>
> >>>
> >>> I can only guess this is part of the response you got from some sos
> >>> request? I cannot reproduce it currently.
> >>>
> >>> So check:
> >>> Does your package pass check if some function names including an
> >>> underscore in the name is returned from an sos request?
> >>
> >>
> >> Hi, Uwe et al.:
> >>
> >>
> >> Thanks, Uwe, for your reply.
> >>
> >>
> >> It's complaining about something in a vignette that has been
> >> part of the package since it appeared in The R Journal in Volume 1/2
> >> in 2009. I received an email from Prof. Ripley complaining that it
> >> reported problems ("WARN") on some of the CRAN checks. When I asked,
> >> Prof. Ripley reply's reply included:
> >>
> >>
> >> >> l.303 {\tt pspline_
> >> >> checker} in the
> >> >> ! ==> Fatal error occurred, no output PDF file produced!
> >> >>
> >> >> Underlines need to be escaped in LaTeX. And as your results
> >> depend on
> >> >> Internet downloads,
> >> >>
> >> >> "Packages which use Internet resources should fail gracefully with
> an
> >> >> informative message if the resource is not available or has changed
> >> >> (and not give a check warning nor error)."
> >> >>
> >> >> applies: you need to anticipate that the results might include
> >> >> underlines.
> >>
> >>
> >> I don't know how to detect, let alone fix the "Underlines" that
> >> "need to be escaped in LaTeX."
> >
> > If you receive an output, postprocess it via
> >
> > gsub("_", "\\\\_", output)
> >
> >
> >
> >>
> >>
> >> Regarding the other issue that "Packages which use Internet
> >> resources should fail gracefully with an informative message if the
> >> resource is not available or has changed (and not give a check warning
> >> nor error)", I assume I should wrap in "try" all tests in *.Rd files
> >> that access the Internet and make sure that they don't fail "R CMD
> >> check" if the Internet is not available.
> >
> > Yes.
> >
> > Best,
> > Uwe Ligges
> >
> >
> >>
> >> Comments?
> >> Thanks again,
> >> Spencer Graves
> >>
> >>
> >> p.s. Yesterday I remember I got "WARN" on three of six CRAN checks
> >> against r-devel on different platforms and NOTE on four of the seven
> >> other CRAN checks. Today I see "WARN" on only two. If I just wait,
> >> these "WARN" problems may go away by themselves. However, Prof.
> >> Ripley gave me other problems to fix, and I want to support our kind,
> >> smart and generous English professor.
> >>
> >>>
> >>> Best,
> >>> Uwe Ligges
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> ! Emergency stop.
> >>>> <inserted text>
> >>>> $
> >>>> l.303 {\tt pspline_
> >>>> checker} in the
> >>>> ! ==> Fatal error occurred, no output PDF file produced!
> >>>> --- failed re-building 'sos.Rnw'
> >>>>
> >>>>
> >>>> I can NOT replicate these locally nor with GitHub action, and
> >>>> I failed to find 'psp' in 'sos.Rnw'.[2] This raises two issue:
> >>>>
> >>>>
> >>>> OBVIOUS: What can I do to fix this error, or at least to understand
> >>>> it better?
> >>>>
> >>>>
> >>>> SUBTLE: How can I configure "github action", so it can replicate
> >>>> the errors reported on CRAN?
> >>>>
> >>>>
> >>>> Thanks,
> >>>> Spencer
> >>>>
> >>>>
> >>>> [1]
> >>>>
> >>>>
> >>>> https://cran.r-project.org
> >>>>
> >>>>
> >>>> [2]
> >>>>
> >>>>
> >>>> https://github.com/sbgraves237/sos
> >>>>
> >>>>
> >>>> -------- Forwarded Message --------
> >>>> Subject: Re: CRAN package sos
> >>>> Date: Sun, 14 May 2023 14:46:06 +0100
> >>>> From: Prof Brian Ripley <rip...@stats.ox.ac.uk>
> >>>> Reply-To: CRAN <c...@r-project.org>
> >>>> To: Spencer Graves <spencer.gra...@prodsyse.com>
> >>>> CC: c...@r-project.org
> >>>>
> >>>> <snip>
> >>>>
> >>>>
> >>>> On 12/05/2023 13:03, Spencer Graves wrote:
> >>>>> Hello, All:
> >>>>
> >>>> You have just spammed my personal email address, contrary to the
> >>>> CRAN policy and done so deliberately and/or recklessly, overriding
> >>>> the Reply-To header.
> >>>>
> >>>>> Is MASS being withdrawn along with multiple other packages
> >>>>> (mgcv, survival, boot, lattice)?
> >>>>
> >>>> Not so. And that was a failure to do your own homework as you
> >>>> should have looked on CRAN to see that they are still available.
> >>>>
> >>>> Further
> >>>>
> >>>> options(repos=c(CRAN="http://cran.cnr.berkeley.edu";))
> >>>>
> >>>> does not respect the user's choice of repository: that seems to make
> >>>> re-making it unreasonably slow. On my very fast MacBook Pro
> >>>>
> >>>> * checking re-building of vignette outputs ...^R
> >>>> [26s/265s] OK
> >>>>
> >>>> so it is waiting 90% of the time.
> >>>>
> >>>>
> >>>>> That's responsible for 3 of the 4 'warnings' listed there.
> >>>>> The warning for r-devel-linux-x86_64-fedora-gcc says "LaTeX errors:
> >>>>> ! Missing $ inserted ... Fatal error occurred, no output PDF file
> >>>>> produced! ... Vignette re-building failed."
> >>>>>
> >>>>>
> >>>>> These all sound to me like operating system errors. If
> >>>>> there's something here I should do, I could use help in
> >>>>> understanding what.
> >>>>
> >>>> Do read the message -- it is a LaTeX error in the LaTeX code your
> >>>> package's vignettes generates.
> >>>>
> >>>> LaTeX errors:
> >>>> ! Missing $ inserted.
> >>>> <inserted text>
> >>>> $
> >>>> l.303 {\tt pspline_
> >>>> checker} in the
> >>>> ! Emergency stop.
> >>>> <inserted text>
> >>>> $
> >>>> l.303 {\tt pspline_
> >>>> checker} in the
> >>>> ! ==> Fatal error occurred, no output PDF file produced!
> >>>>
> >>>> Underlines need to be escaped in LaTeX. And as your results depend
> >>>> on Internet downloads,
> >>>>
> >>>> "Packages which use Internet resources should fail gracefully with
> >>>> an informative message if the resource is not available or has
> >>>> changed (and not give a check warning nor error)."
> >>>>
> >>>> applies: you need to anticipate that the results might include
> >>>> underlines.
> >>>>
> >>>>>
> >>>>>
> >>>>> Thanks,
> >>>>> Spencer Graves
> >>>>> m: 1-408-655-4567
> >>>>>
> >>>>>
> >>>>> On 5/12/23 1:38 AM, Prof Brian Ripley wrote:
> >>>>>> Dear maintainer,
> >>>>>>
> >>>>>> Please see the problems shown on
> >>>>>> <https://cran.r-project.org/web/checks/check_results_sos.html>.
> >>>>>>
> >>>>>> Please correct before 2023-05-26 to safely retain your package on
> >>>>>> CRAN.
> >>>>>>
> >>>>>> The CRAN Team
> >>>>
>
> ______________________________________________
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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