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

[Duncan Murdoch]

On 05/05/2020 10:30 a.m., Martin Maechler wrote:
>>>>>> 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.

We don't have anything to send, so it's hard to say where to send it.

Put together a minimal reproducible example, and it'll probably be easy 
to work out whether it's R, R Markdown, knitr, Pandoc, or LaTeX that has 
the bug.

(Naturally I suspect it's not R, and past experience makes me think it's 
not LaTeX, but there are still three other possibilities in the list.)

Duncan Murdoch

> 
> 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
>      >> number 2742969, whose registered office is 215 Eu...{{dropped:26}}
> 
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