[R] Rgui maintains open file handles after Sweave error

[Alexander Shenkin]

Yep, I'm using RStudio, and have used Tinn-R in the past.  RStudio does
start a new R session when processing a sweave document via the RStudio
GUI.  In my case, this presented a problem for the reasons I stated
before (i.e. that I need to run sweave in the main environment, not a
new one).  Hence, I'm running Sweave from the command line, and
processing the tex doc via TeXworks (from MiKTeX).  I sent the RStudio
team a feature request to add an option to be able to run Sweave in the
main environment (perhaps while maintaining the default of running it in
a separate environment).

Allie

On 4/5/2012 12:12 PM, Yihui Xie wrote:
> 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}
>>>
>>> ______________________________________________
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>>> 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.