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

Patrick Aboyoun paboyoun at fhcrc.org
Thu Apr 10 03:50:26 CEST 2008

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.

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.


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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