Thanks for the nice ideas, Duncan. I think that would work nicely in
most cases. The major issue with that workflow in my case is that the
scripts to set up my workspace take around a half-hour to run (I really
wish CUDA was working with my setup!), so running R each time in that
case is time-consuming.
Perhaps I should be working more with intermediate files, or perhaps
writing the workspace out to an .Rdata file and reading that in the
sweave document instead of running the entire data-prep script.
Thanks,
Allie
On 4/5/2012 11:22 AM, Duncan Murdoch 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@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}
>>
>> ______________________________________________
>> R-help@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.
>
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