[Bioc-devel] BiocCheck warnings and errors

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Tue Sep 13 23:06:42 CEST 2022

On 13/09/2022 13:20, Christian Arnold wrote:

> Didnt the behavior of \donttest change with R 4.0 so that |R CMD check
> --as-cran|now runs|\donttest|examples (see
> https://community.rstudio.com/t/r-cmd-check-r-4-0-0-now-runs-donttest-how-to-proceed-with-long-running-examples/64493)?

That's in the context of 'R CMD check --as-cran', which we don't use. 
AFAIK a bare 'R CMD check' still doesn't run the code in \donttest.

> Not sure whether \donttest or \dontrun is better in a Bioc context.

\donttest should be preferred over \dontrun. The latter should be used 
only for code that is not meant to be run, ever. It doesn't even need to 
be valid code e.g. it could be some pseudo-code that the user would need 
to slightly edit before it works for them. OTOH the former must contain 
valid R code, and that code will be executed when the user tries to run 
the examples in the man page with 'example(<som-alias>)'.



Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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