[Bioc-devel] Is switching to Rmd vignettes a policy? And "polygon edge not found" on macOS error.

[Paul Murrell]

Hi

The technical 'grid' error corresponds to a long-standing 'ggplot2' 
issue that stalled waiting for a simple reproducible example and for me 
to access a MacOS system.  I currently have the latter, but recently 
failed to replicate the problem.

Paul

On 23/01/22 6:29 am, Vincent Carey wrote:
> On Sat, Jan 22, 2022 at 12:12 PM Leonardo Collado Torres <
> lcolladotor using gmail.com> wrote:
> 
>  > Hi everyone,
>  >
>  > The author of `destiny` opened up an issue at `biocthis`
>  > https://github.com/lcolladotor/biocthis/issues/27 
> <https://github.com/lcolladotor/biocthis/issues/27> 
> claiming that all
>  > vignettes need to be changed to Rmd files (aka, use knitr and the 
> vignette
>  > builder engine). I couldn't find such an announcement (and might have
>  > missed it), but maybe there's some type of misunderstanding.
>  >
> 
> Thanks Leo. This came up in conjunction with a package (destiny) that used
> nbconvertR as vignette engine. We in bioc core have decided not to support
> that
> at this time and advised the author to move .ipynb content to inst/...,
> take steps to inform
> users of those resources, and introduce a .Rmd vignette so that destiny is
> consistent
> with general practice.
> 
> There are many .Rnw vignettes in Bioconductor so we can't "require" Rmd but
> I think it is fair to say that Rmd is the de facto standard.
> 
> If there is a technical issue with macos and grid we should address that
> separately. I will try to have a look at this issue soon. I hope others
> will
> look and advise even sooner. :)
> 
> 
>  > As a consequence of trying to change vignettes to Rmd, the author of
>  > `destiny` is running into a `grid` issue best described at
>  > 
> https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-1006736424 
> <https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-1006736424>.
>  > It leads to errors such as "polygon edge not found" only on macOS. The
>  > latest checks at
>  > https://bioconductor.org/checkResults/release/bioc-LATEST/destiny/ 
> <https://bioconductor.org/checkResults/release/bioc-LATEST/destiny> 
> are ok
>  > though on macOS (particularly
>  >
>  > 
> https://bioconductor.org/checkResults/release/bioc-LATEST/destiny/machv2-buildsrc.html 
> <https://bioconductor.org/checkResults/release/bioc-LATEST/destiny/machv2-buildsrc.html>
>  > ).
>  > Though I see that they correspond to
>  >
>  > 
> https://github.com/theislab/destiny/commit/372c3bf1eba2f6278bdf256be56486f75ca58a2a 
> <https://github.com/theislab/destiny/commit/372c3bf1eba2f6278bdf256be56486f75ca58a2a>
>  > which is prior to the commits changing it to Rmd
>  > https://github.com/theislab/destiny/commits/RELEASE_3_14 
> <https://github.com/theislab/destiny/commits/RELEASE_3_14>.
>  >
>  > In any case, has someone else run into this "polygon edge not found" 
> macOS
>  > error? In particular, if there's a system dependency missing, I might 
> have
>  > to update the `biocthis` GitHub Actions (GHA) workflow.
>  >
>  > Thanks in advance.
>  >
>  > Best,
>  > Leo
>  >
>  > Leonardo Collado Torres, Ph. D.
>  > Investigator
>  >
>  > LIEBER INSTITUTE *for* BRAIN DEVELOPMENT
>  > 855 N. Wolfe St., Suite 300
>  > Baltimore, MD 21205
>  > lcolladotor.github.io
>  > lcolladotor using gmail.com
>  >
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>  >
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-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul using stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/