[R] Rgui maintains open file handles after Sweave error

[Duncan Murdoch]

On 04/04/2012 3:25 PM, Alexander Shenkin wrote:
> Hello Folks,
>
> When I run the document below through sweave, rgui.exe/rsession.exe
> leaves a file handle open to the sweave-001.pdf graphic (as verified by
> process explorer).  Pdflatex.exe then crashes (with a Permission Denied
> error) because the graphic file is locked.
>
> This only seems to happen when there is an error in the sweave document.
>   When there are no errors, no file handles are left open.  However, once
> a file handle is stuck open, I can find no other way of closing it save
> for quitting out of R.
>
> Any help would be greatly appreciated!  It would be nice to be able to
> write flawless sweave every time, but flawed as I am, I am having to
> restart R continuously.

I'd suggest a different workflow, in which you run a new copy of R every 
time you want to Sweave a document.  The files will be closed when that 
copy dies, and the results are less likely to be affected by the current 
state of your workspace (assuming you don't load an old workspace in the 
new copy).

For example, when I'm working on a Sweave document, I spend my time in 
my text editor, and get it to run R to process the file whenever I want 
to see what the output looks like.

The only real disadvantages to this approach that I can think of are 
that you need to figure out how to tell your text editor to run R (and 
that might be hard if you're using a poor editor like Windows Notebook, 
but is usually easy), and it will run a tiny bit slower because you need 
to start up R every time.

Duncan Murdoch

> Thanks,
> Allie
>
>
> OS: Windows 7 Pro x64 SP1
>
>
> >  sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
>
> test.Rnw:
>
>      \documentclass{article}
>      \title {file handle test}
>      \author{test author}
>      \usepackage{Sweave}
>      \begin {document}
>      \maketitle
>
>      \SweaveOpts{prefix.string=sweave}
>
>      \begin{figure}
>      \begin{center}
>
>      <<fig=TRUE, echo=FALSE>>=
>          df = data.frame(a=rnorm(100), b=rnorm(100), group = c("g1",
> "g2", "g3", "g4"))
>          plot(df$a, df$y, foo)
>      @
>
>      \caption{test figure one}
>      \label{fig:one}
>      \end{center}
>      \end{figure}
>      \end{document}
>
>
>
> Sweave command run:
>
>      Sweave("test.Rnw", syntax="SweaveSyntaxNoweb")
>
>
>
> Sweave.sty:
>
>      \NeedsTeXFormat{LaTeX2e}
>      \ProvidesPackage{Sweave}{}
>
>      \RequirePackage{ifthen}
>      \newboolean{Sweave at gin}
>      \setboolean{Sweave at gin}{true}
>      \newboolean{Sweave at ae}
>      \setboolean{Sweave at ae}{true}
>
>      \DeclareOption{nogin}{\setboolean{Sweave at gin}{false}}
>      \DeclareOption{noae}{\setboolean{Sweave at ae}{false}}
>      \ProcessOptions
>
>      \RequirePackage{graphicx,fancyvrb}
>      \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
>
>      \ifthenelse{\boolean{Sweave at gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
>      \ifthenelse{\boolean{Sweave at ae}}{%
>        \RequirePackage[T1]{fontenc}
>        \RequirePackage{ae}
>      }{}%
>
>      \DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
>      \DefineVerbatimEnvironment{Soutput}{Verbatim}{}
>      \DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
>
>      \newenvironment{Schunk}{}{}
>
>      \newcommand{\Sconcordance}[1]{%
>        \ifx\pdfoutput\undefined%
>        \csname newcount\endcsname\pdfoutput\fi%
>        \ifcase\pdfoutput\special{#1}%
>        \else\immediate\pdfobj{#1}\fi}
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.