On 03/06/2014, 4:12 AM, Gavin Simpson wrote:
On 2 June 2014 11:44, Duncan Murdoch <murdoch.dun...@gmail.com <mailto:murdoch.dun...@gmail.com>> wrote:On 03/06/2014, 12:58 AM, Yihui Xie wrote: Please also note that I do not expect R core or CRAN maintainers to do any extra work: package authors can easily disable tangle by themselves without anything special flags to R CMD build or R CMD check. The vignettes are still built normally (in terms of "weave"). I brought forward the discussion to hear the possible harm that I was potentially not aware of when we disable tangle for R package vignettes (e.g. does it affect the quality of the package?). So far I have not heard real harm (I admit my judgment is subjective). Several of us have told you the real harm: it means that users can't easily extract a script that replicates the computations done in the vignette. That's a useful thing to be able to do. Isn't the issue here that `tangle()` doesn't, currently, "extract a script that replicates the computations done in the vignette", but rather does so only partially?
No, I think the issue is that some people don't want to have to guarantee that the tangled source produces the same results. R doesn't guarantee it, it is up to the author to do so.
People seem to be arguing across one another throughout this thread. Yihui has identified an infelicity in the tangle implementation. Turning off tangling + sourcing in R CMD check may not be a desirable solution, so if the aim is to extract R code to replicate the computations in the vignette, tangle() needs to be modified to allow for inclusion (optional) of \Sexpr "chunks".
That's one solution, and the other is to limit \Sexpr code to things with no side effects, as Sweave was originally designed.
To move this thread forwards, would contributions that added this optional feature to tangle() be considered by R Core? If so, perhaps those affected by the current infelicity might wish to propose patches to the R sources which implement a solution?
As I said before, I'm more sympathetic to that solution than to dropping the requirement that tangled code should work. I think the changes to base R need only be minimal: only an extra argument to the driver code for the tangling. Users who want to use this feature should write their own (or use someone else's if they don't' mind an extra dependency) as a "non-Sweave vignette driver", whose implementation is to call Stangle with the non-default parameter setting.
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