Yihui, list, Focusing the behavior of R CMD check, the only reason I have seen put forward in the discussion for having check tangle and then source as well as knit/weave the very same vignette is to assist the package maintainer in debugging R errors vs pdflatex errors. As tangle (and many other tools) are already available to an author needing extra help debugging, and as the error messages are usually clear on whether errors come from the R code or whatever format compiling (pdflatex, markdown html, etc), this seems like a poor reason for R CMD check to be wasting time doing two versions of almost (but not literally) the same check.
As has already been discussed, it is possible to write vignettes that can be Sweave'd but not source'd, due to the different treatments of inline chunks. While I see the advantages of this property, I don't see why R CMD check should be enforcing it through the arbitrary mechanism of running both Sweave and tangle+source. If that is the desired behavior for all Sweave documents it should be in part of the Sweave specification not to be able to write/change values in inline expressions, or part of the tangle definition to include inline chunks. I any event I don't see any reason for R CMD check doing both. Perhaps someone can fill in whatever I've overlooked? Carl On Sat, May 31, 2014 at 8:17 PM, Yihui Xie <x...@yihui.name> wrote: > 1. The starting point of this discussion is package vignettes, instead > of R scripts. I'm not saying we should abandon R scripts, or all > people should write R code to generate reports. Starting from a > package vignette, you can evaluate it using a weave function, or > evaluate its derivative, namely an R script. I was saying the former > might not be a bad idea, although the latter sounds more familiar to > most R users. For a package vignette, within the context of R CMD > check, is it necessary to do tangle + evaluate _besides_ weave? > > 2. If you are comfortable with reading pure code without narratives, > I'm totally fine with that. I guess there is nothing to argue on this > point, since it is pretty much personal taste. > > 3. Yes, you are absolutely correct -- Sweave()/knit() does more than > source(), but let me repeat the issue to be discussed: what harm does > it bring if we disable tangle for R package vignettes? > > Sorry if I did not make it clear enough, my priority of this > discussion is the necessity of tangle for package vignettes. After we > finish this issue, I'll be happy to extend the discussion towards > tangle in general. > > Regards, > Yihui > -- > Yihui Xie <xieyi...@gmail.com> > Web: http://yihui.name > > > On Sat, May 31, 2014 at 9:20 PM, Gabriel Becker <gmbec...@ucdavis.edu> > wrote: > > > > > > > > On Sat, May 31, 2014 at 6:54 PM, Yihui Xie <x...@yihui.name> wrote: > > > >> 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/..., > > > > > > It's because .Rnw and Rmd require more from the user than .R. Also, this > > started with vignettes but you seem to be talking more generally. If so, > I > > would point out that not all R code is intended to generate reports, and > > writing pure R code that isn't going to generate a report in an .Rnw/.Rmd > > file would be very strange to say the least. > > > > > >> > >> however, I guess it would be painful to read the pure R script tangled > >> from the source document without the original narratives. > > > > > > That depends a lot on what you want. Reading an woven article/report that > > includes code and reading code are different and equally valid > activities. > > Sometimes I really just want to know what the author actually told the > > computer to do. > > > >> > >> > >> 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. > > > > > > We lose *isolated* code evaluation. Sweave/knit have a lot more moving > > pieces than source/eval do. Many of which are for the purpose of > displaying > > output, rather than running code. > > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Carl Boettiger UC Santa Cruz http://carlboettiger.info/ [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
