[R-SIG-Mac] R 3.1.0: Running 'R CMD Sweave' deletes non tex files created upon batch mode exit

[Marc Schwartz]

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 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