Hi Martin,
Thanks for your confirmation on this.
I normally do not use R CMD Sweave, as I too run under ESS in normal day to day
operations. This finding was a quirk of having a particular Rnw document that I
occasionally run using R CMD Sweave and I had done so over the weekend,
realizing this behavior.
Thanks again.
Regards,
Marc
On Apr 14, 2014, at 7:28 AM, Martin Maechler <maech...@stat.math.ethz.ch> wrote:
>>>>>> Marc Schwartz <marc_schwa...@me.com>
>>>>>> on Sun, 13 Apr 2014 10:22:55 -0500 writes:
>
> [on the R-SIG-Mac mailing list] :
>
>> Hi all,
>> With R version 3.1.0 on OSX, using either the Snow Leopard or the Mavericks
>> binary installation on a Mac with fully updated Mavericks, there has been a
>> change in behavior since 3.0.3.
>
> I've just written to R-core about this:
>
> R CMD Sweave
>
> has *serious* problems also in the very simple case when it
> should produce figures: They are not available after the
> completion of R CMD Sweave,
> confirming your 'deletes non tex files created upon batch mode exit'
>
> So this is not related to OSX only, but also a big problem
> at least on other *nix descendent platforms, such as Linux.
>
> In short, failure (no graphic produce in the example below) by
>
> R CMD Sweave foo.Rnw
>
> but all is fine with using Sweave(), as you Marc, noted, and hence with
>
> Rscript -e 'Sweave("foo.Rnw")'
>
> ... and to answer your question:
> No this was not intended and is probably one of the bigger /
> most embarrassing bugs in a newly released version of R
> in my view:
>
> Basically 'R CMD Sweave' is partly broken in R 3.1.0.
> Yes, this should never have happened.
>
> I had to partially revert the R 3.1.0 installation here (our
> statistics dept), by making R 3.0.3 the default 'R'
> for now, as we are relying on 'R CMD Sweave ..' in many places.
>
> Personally I've never noticed the problem, as I seem to always
> Sweave from ESS (Emacs speaks statistics) which calls Sweave()
> in R, and that works fine, also in R 3.1.0, as you've already
> noted
>
> Martin Maechler, ETH Zurich
>
> %------------------------------------------------------------
> \documentclass[12pt]{article}
> \usepackage{Sweave}
> \begin{document} Just a simple graphic
>
> <<qqnorm, fig=TRUE>>=
> qqnorm(rnorm(20))
> @
>
> and that's all, folks!
> \end{document}
> %------------------------------------------------------------
>
>> I have a master .Rnw file which runs a series of outputs from multiple R
>> code files, each called in BATCH mode using system() from within the master
>> .Rnw file. The output of the R code files go to separate text files in order
>> to catch some of the function call output that would not otherwise be
>> included in the resultant .tex file due to output redirection.
>
>> Those text files are then included in the resultant .tex file using, for
>> example:
>
>> \lstinputlisting[caption={}]{test.out}
>
>> directives which are included in the .Rnw source file.
>
>> A simple example to replicate the observed behaviors.
>
>> The test.Rnw file content:
>
>> %% R CMD Sweave test.Rnw
>> <<results=tex,echo=false>>=
>> system("R CMD BATCH test.R test.out")
>> @
>
>
>> The test.R file content:
>
>> options(echo = FALSE)
>> options(useFancyQuotes = FALSE)
>> installed.packages()
>
>
>> On version 3.0.3, the file test.out is created, along with test.tex.
>> test.out contains the output of installed.packages(). I did not include the
>> aforementioned listing directive in test.Rnw here for simplicity.
>
>> On version 3.1.0, the file test.out is created, but when the R CMD Sweave
>> command exits and returns to the CLI in the console, test.out is deleted,
>> presumably as part of a post R batch session clean up process. The file
>> test.tex is retained.
>
>> I uninstalled 3.1.0 and reinstalled 3.0.3 and observed the prior behavior. I
>> then tried clean installs of both the Snow Leopard and Mavericks 3.1.0
>> binaries, with the new behavior observed in both cases.
>
>> In reading the NEWS file for 3.1.0, there are multiple references to Sweave,
>> but there is nothing explicit about this new behavior.
>
>> I should note that when the .Rnw file is run from within an R 3.1.0
>> interactive session using:
>
>> Sweave("test.Rnw")
>
>> the test.out file is created and not deleted upon the function exit, or when
>> exiting the R session back to the console.
>
>> Thus, this new behavior seems to be limited to running Sweave from the CLI
>> using R CMD. It is not clear to me if this new behavior is by design or
>> perhaps an unintended consequence of changes elsewhere in Sweave processing
>> or in the handling of R in BATCH mode.
>
>> When watching the folder where the file output activity takes place, I note
>> that a file .build.timestamp is created and then deleted, which leads me to
>> believe that the new functions fileSnapshot() and changedFiles() are being
>> used in the course of processing R in BATCH mode. If that is correct and
>> there is a clean up step that is occurring upon BATCH mode exit, which
>> deletes all files and folders other than .tex files, is it possible that
>> this process is being overly aggressive? Or if not, is there a way to not
>> have these files deleted or have a protected folder where these files can be
>> retained?
>
>> Thanks for any insights.
>
>> Regards,
>
>> Marc Schwartz
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