[Bioc-devel] Rmd vignette failures

[Leonardo Collado Torres]

As I was about to hit send, I checked Slack and I found about
https://github.com/Bioconductor/BiocStyle/issues/78. If you are in the
same situation as me, that info will be useful =) + the info on Slack



Original email:



Hi bioc-devel,

Today I got a bunch of emails because most of my packages failed with
errors such as:

Quitting from lines 31-39 (derfinderHelper.Rmd)
Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics:
argument is of length zero

The error basically points to the first R chunk in the Rmd files like
at https://github.com/leekgroup/derfinderHelper/blob/master/vignettes/derfinderHelper.Rmd#L30-L39
for each vignette. I've noticed a similar error in the GitHub Actions
logs for a package I'm actively working on (macOS and Windows using R
from r-lib; Linux using bioc-devel docker still worked details at
https://github.com/LieberInstitute/megadepth/runs/1152833313).

Are you aware of any change to pandoc or markdown that might be
related to this issue? I don't see anything at rstudio/rmarkdown
https://github.com/rstudio/rmarkdown/issues?q=argument+is+of+length+zero.

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