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

[Matthew Young]

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.

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
    > 
    > 
    > 
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-- 
 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 Euston Road, London, NW1 2BE.