The Bioconductor project has a substantial amount of teaching material in the form of Sweave files. For teaching, it can be extremely convenient to give people an R script which they can copy and paste from (or do something else with). This is especially true for inexperienced R users.
Best, Kasper On Sat, May 31, 2014 at 9:54 PM, Yihui Xie <x...@yihui.name> wrote: > I mentioned in my original post that Sweave()/knit()/... can be > considered as the "new" source(). They can do the same thing as > source() does. I agree that fully evaluating the code is valuable, but > it is not a problem since the weave functions do fully evaluate the > code. If there is a reason for why source() an R script is preferred, > I guess it is users' familiarity with .R instead of .Rnw/.Rmd/..., > however, I guess it would be painful to read the pure R script tangled > from the source document without the original narratives. > > So what do we really lose if we turn off tangle? We lose an R script > as a derivative from the source document, but we do not lose the code > evaluation. > > Regards, > Yihui > -- > Yihui Xie <xieyi...@gmail.com> > Web: http://yihui.name > > > On Sat, May 31, 2014 at 6:20 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: > > On 05/31/2014 03:52 PM, Yihui Xie wrote: > >> > >> Note the test has been done once in weave, since R CMD check will try > >> to rebuild vignettes. The problem is whether the related tools in R > >> should change their tangle utilities so we can **repeat** the test, > >> and it seems the answer is "no" in my eyes. > >> > >> Regards, > >> Yihui > >> -- > >> Yihui Xie <xieyi...@gmail.com> > >> Web: http://yihui.name > >> > >> > >> On Sat, May 31, 2014 at 4:54 PM, Gabriel Becker <gmbec...@ucdavis.edu> > >> wrote: > >>> > >>> > >>> > >>> > >>> On Fri, May 30, 2014 at 9:22 PM, Yihui Xie <x...@yihui.name> wrote: > >>>> > >>>> > >>>> Hi Kevin, > >>>> > >>>> > >>>> I tend to adopt Henrik's idea, i.e., to provide vignette > >>>> engines that just ignore tangle. At the moment, it seems R CMD check > > > > > > It is very useful, pedagogically and when reproducing analyses, to be > able > > to source() the tangled .R code into an R session, analogous to running > > example code with example(). The documentation for ?Stangle does read > > > > (Code inside '\Sexpr{}' statements is ignored by 'Stangle'.) > > > > So my 'vote' (recognizing that I don't have one of those) is to > incorporate > > \Sexpr{} expressions into the tangled code, or to continue to flag use of > > Sexpr with side effects as errors (indirectly, by source()ing the tangled > > code), rather than writing engines that ignore tangle. > > > > It is very valuable to all parties to write a vignette with code that is > > fully evaluated; otherwise, it is too easy for bit rot to seep in, or to > > 'fake' it in a way that seems innocent but is misleading. > > > > Martin Morgan > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
