Package vignettes share the same environment?

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?

$ 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

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