Fix tables and Bioconductor build

[TuomasBorman]

Hi!

I noticed that the Bioc devel build fails:

https://bioconductor.org/checkResults/devel/bioc-LATEST/phyloseq/nebbiolo1-buildsrc.html

This is because the vignette build fails:

--- re-building ‘phyloseq-basics.Rmd’ using rmarkdown
YAML parse exception at line 2, column 6,
while scanning a block scalar:
did not find expected comment or line break
Error: processing vignette 'phyloseq-basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 64
--- failed re-building ‘phyloseq-basics.Rmd’

The reason seems to be that pandoc incorrectly interprets the "---" before and after tables as yaml metadata block. (However, I am not sure why this is affecting only devel version as the files seems to be the same; maybe some changes in rendering engines...)

I was able to reproduce the error locally, and it was fixed by adding line breaks between the table and "---". The content seems to be showing as intended.

-Tuomas

[joey711]

Thanks!

…

On Wed, Jan 15, 2025, 01:32 Tuomas Borman ***@***.***> wrote: Hi! I noticed that the Bioc devel build fails: https://bioconductor.org/checkResults/devel/bioc-LATEST/phyloseq/nebbiolo1-buildsrc.html This is because the vignette build fails: --- re-building ‘phyloseq-basics.Rmd’ using rmarkdown YAML parse exception at line 2, column 6, while scanning a block scalar: did not find expected comment or line break Error: processing vignette 'phyloseq-basics.Rmd' failed with diagnostics: pandoc document conversion failed with error 64 --- failed re-building ‘phyloseq-basics.Rmd’ The reason seems to be that pandoc incorrectly interprets the "---" before and after tables as yaml metadata block. (However, I am not sure why this is affecting only devel version as the files seems to be the same; maybe some changes in rendering engines...) I was able to reproduce the error locally, and it was fixed by adding line breaks between the table and "---". The content seems to be showing as intended. -Tuomas ------------------------------ You can view, comment on, or merge this pull request online at: #1777 Commit Summary - 2c2c309 <2c2c309> Fix tables File Changes (1 file <https://github.com/joey711/phyloseq/pull/1777/files>) - *M* vignettes/phyloseq-basics.Rmd <https://github.com/joey711/phyloseq/pull/1777/files#diff-3414bb79ba5620c7aefdb184d9231fc63abef34de41f13e9a01fde9318729745> (8) Patch Links: - https://github.com/joey711/phyloseq/pull/1777.patch - https://github.com/joey711/phyloseq/pull/1777.diff — Reply to this email directly, view it on GitHub <#1777>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGNNXMDC3SBTZP5V767UHL2KYTKLAVCNFSM6AAAAABVGY7EBSVHI2DSMVQWIX3LMV43ASLTON2WKOZSG44DSMRYGY4DCNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>