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

On Sat, Jan 22, 2022 at 12:12 PM Leonardo Collado Torres <
lcolladotor at 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 at gmail.com
 >
 > [[alternative HTML version deleted]]
 >
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 > Bioc-devel at r-project.org mailing list
 > https://stat.ethz.ch/mailman/listinfo/bioc-devel 

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 >

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