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@gin}
\setboolean{Sweave@gin}{true}
\newboolean{Sweave@ae}
\setboolean{Sweave@ae}{true}
\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
\ProcessOptions
\RequirePackage{graphicx,fancyvrb}
\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
\ifthenelse{\boolean{Sweave@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}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
