[Bioc-devel] Is switching to Rmd vignettes a policy? And "polygon edge not found" on macOS error.
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 at r-project.org> on behalf of Paul Murrell <paul at 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.
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.
***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** 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 at 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 at gmail.com > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=oDGXiZZqwQCc4xHP_wRD_qNx24t9TGlZOah61BmivgI&e= > <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=oDGXiZZqwQCc4xHP_wRD_qNx24t9TGlZOah61BmivgI&e= > > > > > -- > The information in this e-mail is intended only for the ...{{dropped:18}} > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=oDGXiZZqwQCc4xHP_wRD_qNx24t9TGlZOah61BmivgI&e= > <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=oDGXiZZqwQCc4xHP_wRD_qNx24t9TGlZOah61BmivgI&e= > -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 paul at stat.auckland.ac.nz https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat.auckland.ac.nz_-7Epaul_&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=Llgr6Ju8hoVA8Q8vIx2JwfTDROX3sIr8NBhhyjiVhns&e= _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=Z0ebTCkEfRj0zYTCYbXuAZTzzpVz2rEFAJPjxhk_bDw&s=oDGXiZZqwQCc4xHP_wRD_qNx24t9TGlZOah61BmivgI&e=