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" <lig...@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.turg...@umanitoba.ca>
> Date: Friday, 1 May 2020 at 20:39
> To: Matthew Young <m...@sanger.ac.uk>, "r-package-devel@r-project.org"
<r-package-devel@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-boun...@r-project.org> on behalf
of Matthew Young <m...@sanger.ac.uk>
> Sent: May 1, 2020 2:24:40 PM
> To: r-package-devel@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.
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>
> 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
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> company registered in England with number 2742969, whose registered
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The Wellcome Sanger Institute is operated by Genome Research
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