[Rd] Bug (?) in vignette handling

[Duncan Murdoch]

On 29/10/2021 5:52 a.m., Martin Maechler wrote:
>>>>>> Duncan Murdoch
>>>>>>      on Thu, 28 Oct 2021 13:18:54 -0400 writes:
> 
>      > This StackOverflow post:  https://stackoverflow.com/q/69756236/2554330
>      > points out that objects created in one vignette are available in a later
>      > vignette.  I don't think this should be happening:  vignettes should be
>      > self-contained.
> 
> I strongly agree.
> 
>      > The current answer there, https://stackoverflow.com/a/69758025/2554330,
>      > suggests that "R CMD check" will detect this.  However, sometimes one
>      > vignette can replace a standard function with a custom version, and then
>      > both will work without generating an error, but the second vignette
>      > won't do the same thing if run independently.
> 
>      > For example, try these pure Sweave vignettes:
> 
>      > -------------------------
>      > aaa3.Rnw:
>      > -------------------------
>      > \documentclass{article}
>      > %\VignetteIndexEntry{Sweave aaa3}
>      > \begin{document}
> 
>      > <<>>=
>      > mean <- function(x) "I am the Sweave mean"
>      > @
> 
>      > \end{document}
> 
>      > ------------------------
>      > aaa4.Rnw:
>      > ------------------------
> 
>      > \documentclass{article}
>      > %\VignetteIndexEntry{Sweave aaa4}
>      > \begin{document}
> 
>      > <<>>=
>      > mean(1:5)
>      > @
> 
>      > \end{document}
> 
>      > Put these in a package, build and install the package, and you'll see
>      > that the mean() function in aaa4.Rnw prints the result from the
>      > redefined mean in aaa3.Rnw.
> 
> Is it because R is *not* run with  --no-save --no-restore
> accidentally?
> Without looking, I would not expect that the vignettes are run
> inside the same running R (even though that may speedup things)
> 

I think for R CMD build they are run in one process, while for R CMD 
check they are in separate processes.  R CMD build runs 
tools::buildVignettes(), which runs code that's part of the vignette 
build engine.

The Sweave engine evaluates things in .GlobalEnv, so any leftover 
objects will be visible there for the next vignette.  I think it's up to 
the writer of each vignette engine whether there's any cleanup, but it 
appears that neither Sweave nor knitr does any.

One possible fix would be for buildVignettes() to make a snapshot of 
what's in .GlobalEnv before processing any vignettes, and restoring it 
after each one.  I've tried a weaker version of this:  it records the 
names in .GlobalEnv at the start, and deletes anything new before 
processing each vignette.  So vignettes could modify or delete what's 
there, but not add anything.

I think you don't want to completely clear out .GlobalEnv, because 
people might choose to run buildVignettes() in an R session and expect 
the vignettes to see the contents there.

"make check" in R-devel doesn't complain about this change, but I'll let 
R Core decide whether it's a good idea or not.  A patch is below.

Duncan Murdoch

Index: src/library/tools/R/Vignettes.R
===================================================================
--- src/library/tools/R/Vignettes.R	(revision 81110)
+++ src/library/tools/R/Vignettes.R	(working copy)
@@ -560,7 +560,11 @@
      sourceList <- list()
      startdir <- getwd()
      fails <- character()
+    # People may build vignettes from a session and expect
+    # to see some variables, so we won't delete these
+    existingVars <- ls(.GlobalEnv, all = TRUE)
      for(i in seq_along(vigns$docs)) {
+    	rm(list = setdiff(ls(.GlobalEnv, all = TRUE), existingVars), envir 
= .GlobalEnv)
          thisOK <- TRUE
          file <- basename(vigns$docs[i])
          enc <- vigns$encodings[i]