[Rd] Bug (?) in vignette handling
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Sun Oct 31 10:31:15 CET 2021
On 30/10/2021 6:11 p.m., Sebastian Meyer wrote:
> Am 30.10.21 um 20:28 schrieb 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.
>
> Thankfully R CMD check has been building the vignettes in separate R
> processes already since R 3.6.0, so has hopefully identified most
> problems until now. The corresponding env var is
> _R_CHECK_BUILD_VIGNETTES_SEPARATELY_.
>
> The standard (and exported!) buildVignettes() has been weaving all
> vignettes in the same session ever since it was added back in 2002. This
> approach is probably more efficient (avoiding repetitive package
> loading), but carry-over effects seem both likely and undesirable
> (thinking of vignettes as separate and independently reproducible
> manuscripts about different aspects of a package). AFAICS, it is not
> explicitly documented that buildVignettes() runs all vignettes in the
> same R session, so at least this is no advertised feature.
>
>> 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.
>
> I think this is by design and also useful in interactive sessions to
> investigate the environment after weaving.
>
>> 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.
>
> Clearing the workspace would be an improvement, but I think it would be
> even better for R CMD build to produce each vignette in a clean R
> session, especially with regard to loaded packages. Changing
> buildVignettes() to use clean R processes by default (I'd say even if
> there is only one vignette) should be considered. I'd appreciate seeing
> this report in Bugzilla to investigate further (and not forget).
Yes, that makes sense: currently R CMD build starts a new clean session
and runs buildVignettes() there; it would make more sense for
buildVignettes to be starting a session for each vignette. Users who
don't want to run their vignettes in a clean session or who want to see
the leftovers can still do so, calling Sweave or knit or whatever directly.
I'll post some of this to Bugzilla.
Duncan Murdoch
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