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

[Leonardo Collado Torres]

Hi everyone,

The author of `destiny` opened up an issue at `biocthis`
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.

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.
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/ are ok
though on macOS (particularly
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
which is prior to the commits changing it to Rmd
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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