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

Patrick Aboyoun paboyoun at fhcrc.org
Thu Apr 10 19:18:54 CEST 2008

Thanks Duncan,
I just did a survey of the BioConductor repository and only 4 of the 354 
.Rnw vignette files contain the \usepackage{Sweave} specification. 
Adding this is tedious, but not impossible. If the \usepackage{Sweave} 
specification does become recommended, could you add a WARNING to the R 
CMD build/check process if a vignette file lacks it? That would help 
steer developers in the right direction for cross-platform compatibility 
since most R package developers don't use Windows as their primary platform.


Duncan Murdoch wrote:
> 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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