[R] Rgui maintains open file handles after Sweave error

[Alexander Shenkin]

Here is Dr. Leisch's advice for dealing with open handles (and it works):

> On 4/5/2012 4:22 AM, Friedrich Leisch wrote:
> ...
> You need to close the pdf device, not an open connection:
>
> R> Sweave("test.Rnw")
> Writing to file test.tex
> Processing code chunks with options ...
>  1 : keep.source term verbatim pdf
>
> Error:  chunk 1
> Error in plot.xy(xy, type, ...) : object 'foo' not found
> R> ls()
> [1] "col.yellowbg" "df"
> R> dev.list()
> pdf
>   2
> R> dev.off()
> null device
>           1
> Best,
> Fritz



On 4/4/2012 2:52 PM, Alexander Shenkin wrote:
> Thanks for the reply, Henrik.  Process Explorer still shows the file
> handle as being open, but R only shows the following:
> 
>> showConnections(all=TRUE)
>   description class      mode text   isopen   can read can write
> 0 "stdin"     "terminal" "r"  "text" "opened" "yes"    "no"
> 1 "stdout"    "terminal" "w"  "text" "opened" "no"     "yes"
> 2 "stderr"    "terminal" "w"  "text" "opened" "no"     "yes"
>>
> 
> On 4/4/2012 2:45 PM, Henrik Bengtsson wrote:
>> See ?closeAllConnections
>>
>> Suggestion to the maintainer of Sweave: "atomify" the figure
>> generation, e.g. use { pdf(); on.exit(dev.off()); {...}; } or similar,
>> instead of { pdf(); {...}; dev.off(); } possibly by leaving a copy of
>> the fault figure file for troubleshooting.
>>
>> /Henrik
>>
>> On Wed, Apr 4, 2012 at 12:25 PM, Alexander Shenkin <ashenkin at ufl.edu> 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.
>>>
>>> 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.