[R-pkg-devel] Rmarkdown vignette yields r inline warning on windows build [EXT]

[Martin Maechler]

>>>>> Matthew Young 
>>>>>     on Mon, 4 May 2020 09:09:55 +0000 writes:

    > I progressively chopped bits out of the vignette till the
    > error stopped to identify the error.  It was being caused
    > by inline latex, where I had two %% marks.  I'm not really
    > sure why this broke things, but removing it fixed it.

"fascinating" .. yes, unfortunately, the Rmarkdown related
engines (I suspect pandoc, but haven't thought or digged about it)
are clearly not bug free.

That's been my experience quite frequently when I "exaggerate"
in my use of LaTeX "tricks" in Rmarkdown documents ..

If somebody knows where exactly such cases should be sent, it
may help improving the situation.. I'm really no expert here.

Martin

    > Thanks,
    > Matthew

    > On 02/05/2020, 16:54, "Uwe Ligges"
    > <ligges using statistik.tu-dortmund.de> wrote:

    >     My wild guess is that 'r ' indicates there is an
    > invisible char after the r that is not representable in
    > the chosen encoding.
    
    >     Best, Uwe Ligges
    
    
    
    >     On 02.05.2020 01:12, Matthew Young wrote:
    >> I’ve tried both ways (with and without a space after the
    >> backtick) and get the same error.
    >> 
    >> From: Max Turgeon <Max.Turgeon using umanitoba.ca> Date:
    >> Friday, 1 May 2020 at 20:39 To: Matthew Young
    >> <my4 using sanger.ac.uk>, "r-package-devel using r-project.org"
    >> <r-package-devel using r-project.org> Subject: Re: Rmarkdown
    >> vignette yields r inline warning on windows build [EXT]
    >> 
    >> 
    >> Since you're looking for suggestions and that's all I
    >> have:
    >> 
    >> 
    >> 
    >> Could it be the space between the tick mark and the r?
    >> For example, does replacing ` round` with `round` (and
    >> all other instances) fix the issue?
    >> 
    >> 
    >> Max Turgeon Assistant Professor Department of Statistics
    >> Department of Computer Science University of Manitoba
    >> maxturgeon.ca
    >> [maxturgeon.ca]<https://urldefense.proofpoint.com/v2/url?u=http-3A__maxturgeon.ca&d=DwMF-g&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XXcY8t_J1mVMCDTmi3629g&m=KD5hkiMRJXvOAV1srKNufKVz3MOekQAmaDIOmgmxB6A&s=AbhQu2y3TVl5oJQLLYAJXIyLZredpV9XsmkkeGsu1Js&e=>
    >> 
    >> 
    >> 
    >> ________________________________ From: R-package-devel
    >> <r-package-devel-bounces using r-project.org> on behalf of
    >> Matthew Young <my4 using sanger.ac.uk> Sent: May 1, 2020
    >> 2:24:40 PM To: r-package-devel using r-project.org Subject:
    >> [R-pkg-devel] Rmarkdown vignette yields r inline warning
    >> on windows build
    >> 
    >> ********************************************************
    >> Caution: This message was sent from outside the
    >> University of Manitoba.
    >> ********************************************************
    >> 
    >> I am trying to submit a package to CRAN that includes a
    >> vignette built using rmarkdown.  It passes fine on the
    >> machines I have access to (ubuntu and osx).  When I
    >> submit to CRAN using the form, it passes the Debian
    >> checks, but fails on windows with the following WARNING:
    >> 
    >> ! Missing $ inserted.  <inserted text> $ l.1030
    >> 
    >> You may need to add $ $ around a certain inline R
    >> expression `r `
    >> 
    >> 
    >> I’m really not sure what is causing this error or how to
    >> debug it.  I do not have any inline r expressions in my
    >> vignette (code here
    >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_constantAmateur_SoupX_blob_devel_vignettes_pbmcTutorial.Rmd&d=DwIDaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XXcY8t_J1mVMCDTmi3629g&m=ES3UP2LbqvhOCSwVRP53v_p9EkdNJSwmYuIlfmKly28&s=R9IaPh1UjnNyLSsE8CxG_GorvzRQPg8160TkSZoRoac&e=
    >> [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_constantAmateur_SoupX_blob_devel_vignettes_pbmcTutorial.Rmd&d=DwMF-g&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XXcY8t_J1mVMCDTmi3629g&m=KD5hkiMRJXvOAV1srKNufKVz3MOekQAmaDIOmgmxB6A&s=1GWJLKyp3TJoM0X6-KWdkBEwtTer6JTOQKvF0d5iSPE&e=>).
    >> I do have back-ticked expression such as `round`, but
    >> they are not executed code.  Can anyone suggest what
    >> might be causing this issue?
    >> 
    >> Many thanks,
    >> 
    >> Matthew
    >> 
    >> 
    >> 
    >> --
    >> The Wellcome Sanger Institute is operated by Genome
    >> Research Limited, a charity registered in England with
    >> number 1021457 and a company registered in England with
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