[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 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. 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 at gmail.com [[alternative HTML version deleted]]
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