On Fri, May 30, 2014 at 9:22 PM, Yihui Xie <xie@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
> is comfortable with vignettes that do not have corresponding R
> scripts, and I hope these R scripts will not become mandatory in the
> future.
>

I'm not sure this is the right approach. This would essentially make the
test optional based on decisions by the package author. I'm not arguing in
favor if this particular test, but if package authors are able to turn a
test off then the test loses quite a bit of it's value.

I think that R CMD check has done a great deal for the R community by
presenting a uniform, minimum "barrier to entry" for R packages. Allowing
package developers to alter the tests it does (other than the obvious case
of their own unit tests) would remove that.

That having been said, it seems to me that tangle-like utilities should
have the option of extracting inline code, and that during R CMD check that
option should *always* be turned on.  That would solve the problem in
question while retaining the test would it not?

~G


>
> Thanks everyone for your comments!
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyihui@gmail.com>
> Web: http://yihui.name
>
>
> On Fri, May 30, 2014 at 8:21 AM, Kevin Coombes
> <kevin.r.coombes@gmail.com> wrote:
> > Hi,
> >
> > Unless someone is planning to change Stangle to include inline
> expressions
> > (which I am *not* advocating), I think that relying on side-effects
> within
> > an \Sexpr construction is a bad idea. So, my own coding style is to
> restrict
> > my use of \Sexpr to calls of the form
> > \Sexpr{show.the.value.of.this.variable}. As a result, I more-or-less
> believe
> > that having R CMD check use Stangle and report an error is probably a
> good
> > thing.
> >
> > There is a completely separate questions about the relationship between
> > Sweave/Stangle or knit/purl and literate programming that is linked to
> your
> > question about whether to use Stangle on vignettes. The underlying
> model(s)
> > in R have drifted away from Knuth's original conception, for some good
> > reasons.
> >
> > The original goal of literate programming was to be able to explain the
> > algorithms and data structures in the code to humans.  For that purpose,
> it
> > was important to have named code chunks that you could move around, which
> > would allow you to describe the algorithm starting from a high level
> > overview and then drilling down into the details. From this perspective,
> > "tangle" was critical to being able to reconstruct a program that would
> > compile and run correctly.
> >
> > The vast majority of applications of Sweave/Stangle or knit/purl in
> modern R
> > have a completely different goal: to produce some sort of document that
> > describes the results of an analysis to a non-programmer or
> > non-statistician.  For this goal, "weave" is much more important than
> > "tangle", because the most important aspect is the ability to integrate
> the
> > results (figures, tables, etc) of running the code into the document that
> > get passed off to the person for whom the analysis was prepared. As a
> > result, the number of times in my daily work that I need to explicitly
> > invoke Stangle (or purl) explicitly is many orders of magnitude smaller
> than
> > the number of times that I invoke Sweave (or knitr).
> >
> >   -- Kevin
> >
> >
> >
> > On 5/30/2014 1:04 AM, Yihui Xie wrote:
> >>
> >> Hi,
> >>
> >> Recently I saw a couple of cases in which the package vignettes were
> >> somewhat complicated so that Stangle() (or knitr::purl() or other
> >> tangling functions) can fail to produce the exact R code that is
> >> executed by the weaving function Sweave() (or knitr::knit(), ...). For
> >> example, this is a valid document that can pass the weaving process
> >> but cannot generate a valid R script to be source()d:
> >>
> >> \documentclass{article}
> >> \begin{document}
> >> Assign 1 to x: \Sexpr{x <- 1}
> >> <<>>=
> >> x + 1
> >> @
> >> \end{document}
> >>
> >> That is because the inline R code is not written to the R script
> >> during the tangling process. When an R package vignette contains
> >> inline R code expressions that have significant side effects, R CMD
> >> check can fail because the tangled output is not correct. What I
> >> showed here is only a trivial example, and I have seen two packages
> >> that have more complicated scenarios than this. Anyway, the key thing
> >> that I want to discuss here is, since the R code in the vignette has
> >> been executed once during the weaving process, does it make much sense
> >> to execute the code generated from the tangle function? In other
> >> words, if the weaving process has succeeded, is it necessary to
> >> source() the R script again?
> >>
> >> The two options here are:
> >>
> >> 1. Do not check the R code from vignettes;
> >> 2. Or fix the tangle function so that it produces exactly what was
> >> executed in the weaving process. If this is done, I'm back to my
> >> previous question: does it make sense to run the code twice?
> >>
> >> To push this a little further, personally I do not quite appreciate
> >> literate programming in R as two separate steps, namely weave and
> >> tangle. In particular, I do not see the value of tangle, considering
> >> Sweave() (or knitr::knit()) as the new "source()". Therefore
> >> eventually I tend to just drop tangle, but perhaps I missed something
> >> here, and I'd like to hear what other people think about it.
> >>
> >> Regards,
> >> Yihui
> >> --
> >> Yihui Xie <xieyihui@gmail.com>
> >> Web: http://yihui.name
>
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>



-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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