[R] Rgui maintains open file handles after Sweave error

[Yihui Xie]

In terms of editors, I think RStudio is pretty good
(http://www.rstudio.org/download/preview). Or LyX
(http://yihui.name/knitr/demo/lyx/), or TeXmaker, WinEdit
(http://yihui.name/knitr/demo/editors/)... All of them start a new R
session when weaving the document, and all support one-click
compilation. In all, anything but Windows Notepad.

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Thu, Apr 5, 2012 at 11:22 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> 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.
>
>
> ______________________________________________
> 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.