On 4/10/2008 1:18 PM, 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.
I think the Sweave default of inserting the path to Sweave.sty is the
problem. I've checked my LaTeX books, and none of them mention this as a
possiblity: the argument of \usepackage is supposed to be a package
name, not a path to a style file with the .sty chopped off. Obviously
some implementations support the syntax of using a path, but this is
clearly not well supported: there's no way I can see to specify
perfectly legal paths, if they happen to contain characters that LaTeX
thinks are special.
So I would say the direction we should move is for Sweave to insert just
\usepackage{Sweave}
(and possibly a comment saying where to go to find it, for people who
don't know how to set up the include path properly). But I wouldn't
make a change like that at this late date for 2.7.0.
Duncan Murdoch
>
>
> 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@r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>
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