[Bioc-devel] build failure due to LaTeX errors on kjohnson3

[Tyler Smith]

Hi,

The build error described below persists on kjohnson3. I can't reproduce it on my local Linux machine, and the package also installs without error on nebbiolo1. It looks like it may be a conflict between the LaTeX file emitted by RMarkdown and the LaTeX programs installed on kjohnson3. I don't know if there's anything I can do at my end to resolve this.

- tyler

On Fri, Apr 17, 2026, at 12:37 PM, Tyler Smith wrote:
> Hi,
>
> I'm getting an error for flowPloidy on kjohnson3:
>
> https://bioconductor.org/checkResults/3.23/bioc-LATEST/flowPloidy/kjohnson3-buildsrc.html
>
> ```
> * creating vignettes ... ERROR
> --- re-building ‘flowPloidy-gettingStarted.Rmd’ using rmarkdown
> ! LaTeX Error: Lonely \item--perhaps a missing list environment.
>
> Error: processing vignette 'flowPloidy-gettingStarted.Rmd' failed with 
> diagnostics:
> LaTeX failed to compile 
> /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmploH5TV/Rbuilde12c69dd085d/flowPloidy/vignettes/flowPloidy-gettingStarted.tex. 
> See https://yihui.org/tinytex/r/#debugging for debugging tips. See 
> flowPloidy-gettingStarted.log for more info.
> --- failed re-building ‘flowPloidy-gettingStarted.Rmd’
> ```
>
> I haven't changed the vignettes in several releases, and I'm not 
> manually creating LaTeX - it's all generated from Rmd by RMarkdown. The 
> vignettes compile without error on my local machine as well as 
> nebbiolo1 and kunpeng2.
>
> Any advice on how to resolve this would be appreciated!
>
> (I know there are currently Warnings on the Linux machines; these 
> should be fixed with the last commit I uploaded yesterday).
>
> - tyler
>
> -- 
> plantarum.ca
>
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