From Kurt.Hornik at wu-wien.ac.at  Thu Apr 10 21:07:38 2008
From: Kurt.Hornik at wu-wien.ac.at (Kurt Hornik)
Date: Thu, 10 Apr 2008 21:07:38 +0200
Subject: [Rd] Windows problem related to using shortPathName for Sweave
 style file
In-Reply-To: <alpine.LFD.1.00.0804101848250.20043@gannet.stats.ox.ac.uk>
References: <47FD3032.7020709@fhcrc.org> <47FD33E2.8090300@fhcrc.org>
	<47FD56AA.4030707@stats.uwo.ca> <47FD7262.9060901@fhcrc.org>
	<47FE05F1.2030507@stats.uwo.ca> <47FE4BFE.1060902@fhcrc.org>
	<alpine.LFD.1.00.0804101848250.20043@gannet.stats.ox.ac.uk>
Message-ID: <18430.25978.513720.319931@fangorn.hornik.net>

>>>>> Prof Brian Ripley writes:

> I suggest that we try to program a solution in Sweave.  It only inserts 
> the path to the file is stylepath=TRUE in RweaveLatexSetup, so it seems 
> to be that

> Sweave(stylepath=FALSE)

> is all that is needed.  That seems to work, although of course obliges 
> people to make sure Sweave.sty is in their latex input path (and using 
> texi2dvi makes that rather hard).

Unless you do

  R CMD texi2dvi

as this will add the R share/texmf to TEXINPUTS.

> Sweave is only used by R in three places, in 
> tools:::.install_package_vignettes which is only used to build the grid 
> vignettes, and tools::checkVignettes (used by R CMD check) and 
> buildVignettes (used by R CMD build), and none of which pass any arguments 
> to Sweave.

> Here's a proposal.  Instead of making stylepath=TRUE the default, set its 
> default from the environment variable _SWEAVE_STYLEPATH_DEFAULT_ . Then 
> all Patrick needs to do is to set this to FALSE and ensure that his MiKTeX 
> setup has Sweave.sty in a texmf tree.

> That leaves the question of what the default should be if the environment 
> variable is not set -- I suggest TRUE unless the path contains a space 
> (since it doesn't currently work if it does and so is backwards 
> compatible).

> That seems well below the limits of what is acceptable at this point for 
> 2.7.0, so if reaction is favourable we should go ahead.

Personally, I always thought the default should be not to set the path
and suggest to use R CMD texi2dvi.

Best
-k

> Brian Ripley

> On Thu, 10 Apr 2008, Patrick Aboyoun wrote:

>> 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.
>> 
>> 
>> Cheers,
>> Patrick
>> 
>> 
>> 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}
>>>>> ?
>>>>>> 
>>>>>> 
>>>>> ------------------------------------------------------------------------
>>>>>> 
>>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>> 
>>> 
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 

> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595

> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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