[Bioc-devel] Timeout on package builder: R CMD build-specific issue

[Benjamin Jean-Marie Tremblay]

Hi,

Recently my package (universalmotif) has suddenly started timing out on both release and devel builds for all platforms (https://bioconductor.org/checkResults/devel/bioc-LATEST/universalmotif/), stopping at the "creating vignettes" stage. I've determined that the issue is this particular line in one of the vignettes which hangs indefinitely:

https://github.com/bjmt/universalmotif/blob/master/vignettes/MotifComparisonAndPvalues.Rmd#L27

However, I cannot understand why... Compiling the vignette from within R on my laptop with rmarkdown::render works fine, and the code runs instantly by itself in my terminal. My package hasn't been updated with any code changes recently, and as far as I can tell neither has any dependency which touches this part of the code.

Does anyone happen to know why R CMD build elicits such different behaviour compared to interactively running the code? I can confirm that the hang occurs locally when using R CMD build, so it's not specific to the Bioc machines as far as I can tell. Unfortunately I haven't had any success finding any information about this particular kind of issue.

Thanks in advance,

Benjamin

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