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

Mon Jan 24 18:21:12 CET 2022

Herve documented the `polygon edge not found` error at https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-macOS-Mojave-HOWTO.md#major-issue-fontsxquartz-issue-on-macos-high-sierra-or-higher, including reproducible examples and the hack we use on the build system.

Reproducible example:

library(ggplot2)
png(tempfile(), type="quartz")
ggplot(data.frame(), aes(1, 1))
dev.off()

The hack we use on the build system is to put `options(bitmapType="cairo")` at the beginning of the `local({})` block in `/Library/Frameworks/R.framework/Resources/library/grDevices/R/grDevices`.

See the BBS documentation for more explanation.

Jennifer Wokaty
Bioconductor Core Team

________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Paul Murrell <paul using stat.auckland.ac.nz>
Sent: Sunday, January 23, 2022 3:30 PM
To: Vincent Carey; Leonardo Collado Torres
Cc: Bioc-devel
Subject: Re: [Bioc-devel]  Is switching to Rmd vignettes a policy? And "polygon edge not found" on macOS error.

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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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lcolladotor_biocthis_issues_27&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=xViUwp7MZYhNpvEwi2xBe4rPaegp6106e_P_SyW3eEM&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lcolladotor_biocthis_issues_27&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=xViUwp7MZYhNpvEwi2xBe4rPaegp6106e_P_SyW3eEM&e= >
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tidyverse_ggplot2_issues_2252-23issuecomment-2D1006736424&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=LBF0xRv52hwU6gbW52xiYt0e2lj5a_SjH_QNaOhV3vg&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tidyverse_ggplot2_issues_2252-23issuecomment-2D1006736424&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=LBF0xRv52hwU6gbW52xiYt0e2lj5a_SjH_QNaOhV3vg&e= >.
>  > It leads to errors such as "polygon edge not found" only on macOS. The
>  > latest checks at
>  > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_destiny_&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=F7eoV4JuHlZS-VjLxCXxpAZJD0RRzx9BYPd3GOoSMLI&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_destiny&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=79O48Sy9ntzKzadBAD3ohIJHnCrpjX9OvgJF6K0iwVM&e= >
> are ok
>  > though on macOS (particularly
>  >
>  >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_destiny_machv2-2Dbuildsrc.html&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=vM-sZbjq-dOvarc3KU_JL5pZ57YALm_kZIk9bCT0YGA&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_destiny_machv2-2Dbuildsrc.html&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=vM-sZbjq-dOvarc3KU_JL5pZ57YALm_kZIk9bCT0YGA&e= >
>  > ).
>  > Though I see that they correspond to
>  >
>  >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_theislab_destiny_commit_372c3bf1eba2f6278bdf256be56486f75ca58a2a&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=JRj1XmprB5Q7kbHmQlYEwxmSwTr4l4--WEkJ3JBPeZI&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_theislab_destiny_commit_372c3bf1eba2f6278bdf256be56486f75ca58a2a&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=JRj1XmprB5Q7kbHmQlYEwxmSwTr4l4--WEkJ3JBPeZI&e= >
>  > which is prior to the commits changing it to Rmd
>  > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_theislab_destiny_commits_RELEASE-5F3-5F14&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=4L_5_JXVJjFZKg0jtdhMIKecuGeMqSZf-1q4paZJGVE&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_theislab_destiny_commits_RELEASE-5F3-5F14&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=4L_5_JXVJjFZKg0jtdhMIKecuGeMqSZf-1q4paZJGVE&e= >.
>  >
>  > 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
>  >
>  > [[alternative HTML version deleted]]
>  >
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--
Dr Paul Murrell
Department of Statistics
The University of Auckland
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