From murdoch at stats.uwo.ca  Thu Apr 10 01:52:10 2008
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Wed, 09 Apr 2008 19:52:10 -0400
Subject: [Rd] Windows problem related to using shortPathName for Sweave
 style file
In-Reply-To: <47FD33E2.8090300@fhcrc.org>
References: <47FD3032.7020709@fhcrc.org> <47FD33E2.8090300@fhcrc.org>
Message-ID: <47FD56AA.4030707@stats.uwo.ca>

On 09/04/2008 5:23 PM, Patrick Aboyoun wrote:
> Something funky happened to my e-mail. I was trying to paste information 
> related to MiKTeX and R into my message and it appears to have corrupted 
> the text somehow. Anyway, the message I was trying to get across is that 
> the tex file contains the path
> 
> \usepackage{E:/paboyoun/BBS-2~1.2-B/R/share/texmf/Sweave}
> 
> and MiKTeX 2.7 doesn't know how to resolve it. (The Bioconductor.tex 
> file is (hopefully) attached to this e-mail.)

You should be able to get things to work by explicitly putting

\usepackage{Sweave}

somewhere early in your .Rnw file.  You may have trouble with MikTeX 
finding Sweave.sty, depending how you invoke it:  if invoked from R CMD 
it should work, but maybe not from your command line unless you tell it 
where to look for include files.  How you do that changes all the time; 
R tries a couple, which is why R CMD probably works.

Duncan Murdoch

> 
> 
> === BEGIN OS BLOCK ===
> 
> E:\paboyoun>pdflatex --version
> MiKTeX-pdfTeX 2.7.2987 (1.40.7) (MiKTeX 2.7)
> Copyright (C) 1982 D. E. Knuth, (C) 1996-2006 Han The Thanh
> TeX is a trademark of the American Mathematical Society.
> 
> E:\paboyoun>pdflatex Bioconductor.tex
> This is pdfTeX, Version 3.141592-1.40.7 (MiKTeX 2.7)
> entering extended mode
> (Bioconductor.tex
> LaTeX2e <2005/12/01>
> Babel <v3.8h> and hyphenation patterns for english, dumylang, 
> nohyphenation, ge
> rman, ngerman, french, loaded.
> ("C:\Program Files\MiKTeX 2.7\tex\latex\base\article.cls"
> Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
> ("C:\Program Files\MiKTeX 2.7\tex\latex\base\size12.clo"))
> ("C:\Program Files\MiKTeX 2.7\tex\latex\psnfss\times.sty")
> ("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hyperref.sty"
> ("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\keyval.sty")
> ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\hycolor.sty")
> ("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\pd1enc.def")
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\etexcmds.sty"
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\infwarerr.sty"))
> ("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\hyperref.cfg")
> ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\kvoptions.sty")
> Implicit mode ON; LaTeX internals redefined
> ("C:\Program Files\MiKTeX 2.7\tex\latex\ltxmisc\url.sty")
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bitset.sty"
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\intcalc.sty")
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bigintcalc.sty"
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\pdftexcmds.sty")))
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\kvsetkeys.sty")
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\atbegshi.sty"
> ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifpdf.sty")))
> *hyperref using default driver hpdftex*
> ("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hpdftex.def")
> ! Missing \endcsname inserted.
> <to be read again>
>                    \protect
> l.28 \begin
>            {document}
> ?
> 
> 
> ------------------------------------------------------------------------
> 
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[Rd] Windows problem related to using shortPathName for Sweave style file
Duncan Murdoch