From murdoch.duncan at gmail.com  Sun Nov  2 16:10:05 2014
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Sun, 02 Nov 2014 10:10:05 -0500
Subject: [Rd] package vignettes build in the same R process?
In-Reply-To: <54557E5A.7090800@fredhutch.org>
References: <54557E5A.7090800@fredhutch.org>
Message-ID: <5456494D.9020702@gmail.com>

On 01/11/2014, 8:44 PM, Martin Morgan wrote:
> If I understand correctly, all vignettes in a package are built in the same R 
> process. Global options, loaded packages, etc., in an earlier vignette persist 
> in later vignettes. This can introduce user confusion (e.g., when a later 
> vignette builds successfully because a package is require()'ed in an earlier 
> vignette, but not the current one), difficult-to-identify bugs (e.g., when
> a setting in an earlier vignette influences calculation in a latter vignette), 
> and misleading information about reproducibility (e.g., when the sessionInfo() 
> of a later vignette reflects packages used in earlier vignettes).
> 
> I believe the relevant code is at
> 
> src/library/tools/R/Vignettes.R:505
> 
>          output <- tryCatch({
>              ## FIXME: run this in a separate process
>              engine$weave(file, quiet = quiet)
>              setwd(startdir)
>              find_vignette_product(name, by = "weave", engine = engine)
>          }, error = function(e) {
>              stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",
>                   file, conditionMessage(e)), domain = NA, call. = FALSE)
>          })
> 
> Is building of each vignette in separate processes a reasonable feature request?

I'm not sure.  It's not perfect:  users may still see different output
than the package contains, because when they run the vignette it will
see their system state, but at least it gives them a way to get the
identical output.  On the other hand, they already have a way to do
that:  just build the whole package.  Overall I'd say it's probably a
good idea.

I would prefer a way to detect and warn when vignette output depends on
the state outside the vignette, but that looks hard to do.

Duncan Murdoch



[Rd] package vignettes build in the same R process?
Duncan Murdoch