On 05/04/2014, 2:24 PM, Martin Morgan wrote:
In a package 'vig' R CMD build vig (or tools::buildVignettes(dir="vig") with$ cat vig/vignettes/vig1.Rnw \documentclass{article} \begin{document} <<>>= x <- 1 @ \end{document} $ cat vig/vignettes/vig2.Rnw \documentclass{article} \begin{document} <<>>= x @ \end{document} produces vig2.pdf where x is defined with value 1 -- the vignettes share a build environment. This seems undesirable in terms of reproducibility (a reader of vig2.pdf will not understand where x is assigned; similarly for the results of require() or data() in vig1 referenced in vig2), and is not (?) documented. A more elaborate context is https://stat.ethz.ch/pipermail/bioc-devel/2014-April/005501.html Would it be better to build each vignette in its own environment?
It's not just the environment that gets shared: if you run buildVignette or buildVignettes in an R session, other aspects of the session (e.g. options() settings) will also be inherited by the vignette. The way "R CMD build" handles this is to start a new R process to build the vignettes.
Currently it builds all vignettes in one process, rather than starting a separate process for each, which is why you see the x variable carry from one vignette to another. I think it has been like this for quite a while, because on some platforms (e.g. Windows), starting a new process is quite slow.
I don't know if any other packages than gage currently depend on this behaviour. It does sound confusing for the reader, but I don't think it breaks reproducibility: after all, if a user has the package, they have all the vignettes, not just one. If they just have the vignette, then they might not have the functions in the package that it needs, so they've already lost reproducibility.
Duncan Murdoch
$ R --version|head -n 3 R version 3.1.0 RC (2014-04-05 r65379) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) Martin
______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
