Re: [R] Newbie help with Sweave

From: James W. MacDonald <jmacdon_at_med.umich.edu>
Date: Tue, 25 Mar 2008 10:06:54 -0400

Hi Kevin,

I usually install R in e.g., C:\R-2.6.2 to avoid such problems.

Best,

Jim

Zembower, Kevin wrote:

> Kevin, thanks for writing. Yes, sorry, I forgot to mention that this is
> a Windows XP Professional system running GNU Emacs 22.1.1
> (i386-mingw-nt5.1.2600) from Vincent Goulet, and R 2.6.2 Windows
> version. I pasted in the sessionInfo() output from ESS inside of Emacs
> to the end of this note.
> 
> Was your TA successful in correcting this error? How? Should I report
> this to R-development as something worth fixing for the next release?
> 
> Thanks, again, for your response and advice.
> 
> -Kevin
> 
> 
> 
> -----Original Message-----
> From: Kevin E. Thorpe [mailto:kevin.thorpe_at_utoronto.ca] 
> Sent: Monday, March 24, 2008 9:01 PM
> To: Zembower, Kevin
> Cc: r-help_at_stat.math.ethz.ch
> Subject: Re: [R] Newbie help with Sweave
> 
> Is this in a windows system?  A TA of mine was just getting the exact
> same message.  He tracked it down to the pathname for Sweave.sty having
> trouble with "Program Files" in the path.
> 
> Kevin
> 
> Zembower, Kevin wrote:

>> I think I've gotten my Emacs/Sweave/R system set up correctly, thanks
> to

>> Vincent and Jim, but I haven't been successful getting my first
> document

>> produced. I'm trying to use one of Friedrich Leisch's examples,
>> http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw. I cut and
>> pasted the text into a document sweaveexample.Rnw in Emacs. It seemed
> to

>> be processed successfully with R:
>>> Sweave("sweaveexample.Rnw")
>> Writing to file sweaveexample.tex
>> Processing code chunks ...
>>
>> You can now run LaTeX on 'sweaveexample.tex'

>>
>> However, when I try to open the file sweaveexample.tex and process it
>> with Latex in Emacs, I get this error:
>> ERROR: Missing \endcsname inserted.

>>
>> --- TeX said ---
>> <to be read again>
>> \protect
>> l.7 \begin
>> {document}
>> --- HELP ---
>> >From the .log file...
>>
>> The control sequence marked <to be read again> should
>> not appear between \csname and \endcsname.

>>
>> I've tried a variety of examples, but the error messages are the same.

>>
>> Can anyone point out my errors or mistakes? I've pasted in the full
>> files below. Thanks so much for your help and advice.

>>
>> -Kevin
>>
>> Kevin Zembower
>> Internet Services Group manager
>> Center for Communication Programs
>> Bloomberg School of Public Health
>> Johns Hopkins University
>> 111 Market Place, Suite 310
>> Baltimore, Maryland 21202
>> 410-659-6139
>> ==============================
>> sweaveexample.tex:
>> ==============================
>> \documentclass[a4paper]{article}

>>
>> \title{Sweave Example 1}
>> \author{Friedrich Leisch}
>>
>> \usepackage{C:/PROGRA~1/R/R-26~1.2/share/texmf/Sweave}
>> \begin{document}

>>
>> \maketitle
>>
>> In this example we embed parts of the examples from the
>> \texttt{kruskal.test} help page into a \LaTeX{} document:
>>
>> \begin{Schunk}
>> \begin{Sinput}

>>> data(airquality)
>>> library(ctest)
>>> kruskal.test(Ozone ~ Month, data = airquality)
>> \end{Sinput}
>> \begin{Soutput}
>> Kruskal-Wallis rank sum test
>>
>> data: Ozone by Month
>> Kruskal-Wallis chi-squared = 29.2666, df = 4, p-value = 6.901e-06
>> \end{Soutput}
>> \end{Schunk}
>> which shows that the location parameter of the Ozone
>> distribution varies significantly from month to month. Finally we
>> include a boxplot of the data:

>>
>> \begin{center}
>> \includegraphics{sweaveexample-002}
>> \end{center}

>>
>> \end{document}
>> ================================
>> sweaveexample.Rnw:
>> ==============================
>> \documentclass[a4paper]{article}
>>
>> \title{Sweave Example 1}
>> \author{Friedrich Leisch}
>>
>> \begin{document}
>>
>> \maketitle
>>
>> In this example we embed parts of the examples from the
>> \texttt{kruskal.test} help page into a \LaTeX{} document:
>>
>> <<>>=
>> data(airquality)
>> library(ctest)
>> kruskal.test(Ozone ~ Month, data = airquality)
>> @
>> which shows that the location parameter of the Ozone
>> distribution varies significantly from month to month. Finally we
>> include a boxplot of the data:
>>
>> \begin{center}
>> <<fig=TRUE,echo=FALSE>>=
>> boxplot(Ozone ~ Month, data = airquality)
>> @
>> \end{center}

>>
>> \end{document}
>
>
-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

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