Carl, I don't really have a horse in this race other than a strong feeling that whatever check does should be mandatory.
That having been said, I think it can be argued that the fact that check does this means that it IS in the R package vignette specification that all vignettes must be such that their tangled code will run without errors. ~G On Sun, Jun 1, 2014 at 8:43 PM, Carl Boettiger <cboet...@gmail.com> wrote: > 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/ > -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
