[Rd] Windows problem related to using shortPathName for Sweave style file

Duncan Murdoch murdoch at stats.uwo.ca
Thu Apr 10 14:20:01 CEST 2008

On 4/9/2008 9:50 PM, Patrick Aboyoun wrote:
> I forgot to mention the BioConductor Windows build machine is running
> Microsoft Windows Server 2003 R2
> Enterprise Edition, SP2
> I just checked and this same problem exists if I place R in the standard 
> "C:\Program Files\R" location on this machine.

We're going to roll back that change, so you should be okay with your 
original setup.  As far as I know there is no way to get MikTeX to work 
if you have a space in your pathname, so putting R in the standard 
location will fail, unless you follow the advice I give below.

> For now the backup plan is to move to using short path names for 
> BioConductor builds (modifying 100+ vignettes is impractical as well as 
> configuring MiKTeX to handle multiple installs of R that the build 
> machine uses). If there is an alternate configuration that I should be 
> using, just let me know.

I would recommend biting the bullet and adding \usepackage{Sweave} to 
every vignette.  It's just a one line addition to them, and it will mean 
that their .tex output will work if you move it to a different machine, 
where the full path to Sweave.sty is different.

Duncan Murdoch

> Cheers,
> Patrick
> Duncan Murdoch wrote:
>> 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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