>>>>> Martin Morgan <martin.mor...@roswellpark.org> >>>>> on Sun, 15 May 2016 14:25:01 -0400 writes:
> On 05/15/2016 02:20 PM, Dan Tenenbaum wrote: >> >> >> ----- Original Message ----- >>> From: "Richard Cotton" <richiero...@gmail.com> To: >>> "bioc-devel" <bioc-devel@r-project.org> Sent: Sunday, >>> May 15, 2016 4:45:09 AM Subject: [Bioc-devel] \donttest >>> and the "80% of man pages documenting exported objects >>> must have runnable examples" rule >> >>> I have a package with a lot of examples in exported >>> functions marked as \donttest. >>> >>> BiocCheck doesn't count these functions towards the >>> target of having 80% of exported objects with runnable >>> examples. I do have more than 80% runnable examples; >>> it's just that BiocCheck can't see them. (For >>> background, the package is mostly about file import, and >>> it takes a second or two to import the sample files >>> included in the package. Having examples that run for a >>> couple of seconds is fine for users, but makes package >>> testing very slow (once dozens of the example are run). >>> >>> This check is considered REQUIRED to be solved, so I'd >>> like to know if it's OK to include an explanation about >>> the use of \donttest during submission, or if my pacakge >>> will just get rejected outright. >>> >> >> >> Ultimately, humans make all decisions about package >> inclusion. So you will have a chance to discuss your >> package with someone. > Examples traditionally have dual roles in illustrating > functionality and testing code. It would be particularly > favorable if you could point to other parts of your > package where the code was tested -- unit tests via RUnit > or testthat being a natural place, see > http://bioconductor.org/developers/how-to/unitTesting-guidelines/ > -- and it's use illustrated -- vignettes or other > examples. > Martin I also wonder *why* you use \donttest{} so extensively. It's clearly better than \dontrun{} (which really distresses me, if used more than occasionally). I was involved 20 years ago ensuring that in R, almost all help pages have examples *and* that all examples ran, and you could use example(<..>) to let them run, get quickly some example objects into your R session, etc, etc, etc. Hence, I've recently felt chagrined repeatedly, seeing package authors providing whole packages with no runnable examples.. the other Martin M (Martin Maechler, ETH Zurich) _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel