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

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Sat Jan 22 18:29:17 CET 2022

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 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
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
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
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.
> 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
> 855 N. Wolfe St., Suite 300
> Baltimore, MD 21205
> lcolladotor.github.io
> lcolladotor using gmail.com
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

The information in this e-mail is intended only for the ...{{dropped:18}}

More information about the Bioc-devel mailing list