[R] package Utils Sweave Example Error

Prof Brian Ripley ripley at stats.ox.ac.uk
Fri Oct 17 16:52:37 CEST 2008 

The default for this has been changed for R 2.8.0.  The fix is also 
available in 2.7.x:

(2.8.0:)
     o	The default for 'stylepath' in Sweave's (default) RweaveLatex
 	driver is now FALSE rather than TRUE if
 	SWEAVE_STYLEPATH_DEFAULT is unset : see ?RweaveLatex.
 	To support this, tools::texi2dvi adds the R 'texmf' directory
 	to the input search path.

(2.7.0:)

     o	The default for 'stylepath' in Sweave's (default) RweaveLatex
 	driver can be set by the environment variable
 	SWEAVE_STYLEPATH_DEFAULT: see ?RweaveLatex.

On Fri, 17 Oct 2008, Duncan Murdoch wrote:

> On 10/17/2008 9:24 AM, Thompson, David (MNR) wrote:
>> (Question/suggestion inline below) 
>>> -----Original Message-----
>>> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca] Sent: October 16, 2008 
>>> 02:17 PM
>>> To: mazatlanmexico at yahoo.com
>>> Cc: r-help at stat.math.ethz.ch
>>> Subject: Re: [R] package Utils Sweave Example Error
>>> 
>>> On 10/16/2008 12:19 PM, Felipe Carrillo wrote:
>>>> This is my sessionInfo() and Sys.getenv("PATH")
>>>>   library(tools)
>>>> testfile <- system.file("Sweave", "Sweave-test-1.Rnw", 
>>> package = "utils")
>>>> ## enforce par(ask=FALSE)
>>>> options(device.ask.default=FALSE)
>>>> ## create a LaTeX file
>>>> Sweave(testfile)
>>>> Writing to file Sweave-test-1.tex
>>>> Processing code chunks ...
>>>>  1 : print term verbatim
>>>>  2 : term hide
>>>>  3 : echo print term verbatim
>>>>  4 : term verbatim
>>>>  5 : echo term verbatim
>>>>  6 : echo term verbatim eps pdf
>>>>  7 : echo term verbatim eps pdf
>>>> 
>>>> You can now run LaTeX on 'Sweave-test-1.tex'
>>>> ## This can be compiled to PDF by
>>>> texi2dvi("Sweave-test-1.tex", pdf=TRUE,quiet=FALSE)
>>>> 
>>>> This is pdfTeX, Version 3.1415926-1.40.9 (MiKTeX 2.7)
>>>> entering extended mode
>>>> ("C:/Program Files/R/R-2.7.2/bin/Sweave-test-1.tex"
>>>> LaTeX2e <2005/12/01>
>>>> Babel <v3.8l> and hyphenation patterns for english, 
>>> dumylang, nohyphenation, ge
>>>> rman, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, 
>>> 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\size10.clo"))
>>>> ("C:\Program Files\MiKTeX 2.7\tex\latex\ltxmisc\a4wide.sty"
>>>> ("C:\Program Files\MiKTeX 2.7\tex\latex\ntgclass\a4.sty"))
>>>> ! Missing \endcsname inserted.
>>>> <to be read again>                    \protect l.11 \begin
>>>>            {document}
>>>> ? pdflatex.EXE: Bad file descriptor
>>> 
>>> 
>>> This appears to be the problem.  I'm not certain, but I would guess if you 
>>> look in the "C:/Program Files/R/R-2.7.2/bin/Sweave-test-1.tex" file you'll 
>>> see a line something like this:
>>> 
>>> \usepackage{C:/Program Files/R/R-2.7.2/share/texmf/Sweave}
>>> 
>>> That line (which was added by Sweave) will not work, because LaTeX does 
>>> not understand blanks in file paths.  There are a couple of workarounds:
>> 
>> Does the Windoze convention of using "C:/Progra~1/" to represent
>> "C:/Program Files/" not work in these situations?
>
> No, it doesn't work.  I think LaTeX doesn't like tildes in filenames any more 
> than it likes spaces.  In fact, I think I got it wrong: we actually insert 
> something like
>
> \usepackage{C:/PROGRA~1/R/R-27~1.2/share/texmf/Sweave}
>
> But if we had inserted a path with spaces we would have seen the same error 
> message.
>
> This is clearly a LaTeX or MikTeX problem, not an R or Windows problem.  The 
> workarounds I gave appear to be the best solutions.
>
> Duncan Murdoch
>
>> 
>> DaveT.
>> *************************************
>> Silviculture Data Analyst
>> Ontario Forest Research Institute
>> Ontario Ministry of Natural Resources
>> david.john.thompson at ontario.ca
>> http://ontario.ca/ofri
>> *************************************
>> 
>>> 
>>> 1.  Install R in a directory that doesn't contain blanks.
>>> 
>>> 2.  Include \usepackage{Sweave} in the Rnw file you're processing; this 
>>> will stop Sweave from adding anything.  I believe we set things up so that 
>>> MikTeX will find it in the right place (though I don't normally use 
>>> texi2dvi, so I'm not sure).
>>> 
>>> To test this, you can just go and edit the Sweave-test-1.tex file now, 
>>> replacing the long line with the short version.
>>> 
>>> Duncan Murdoch
>>> 
>>>> texify: pdflatex failed for some reason (see log file).
>>>> Error in texi2dvi("Sweave-test-1.tex", pdf = TRUE, quiet = FALSE) : 
>>>> running 'texi2dvi' on 'Sweave-test-1.tex' failed
>>>> 
>>>> sessionInfo()
>>>> R version 2.7.2 (2008-08-25) i386-pc-mingw32 
>>>> locale:
>>>> LC_COLLATE=English_United 
>>> States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United 
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>> 
>>>> attached base packages:
>>>> [1] tools     stats     graphics  grDevices utils 
>>> datasets  methods   base 
>>>>> Sys.getenv("PATH") 
>>>> PATH
>>>> "C:\\Program Files\\MiKTeX 
>>> 2.7\\miktex\\bin;C:\\GTK\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS
>>> ;C:\\WINDOWS\\System32\\Wbem;C:\\Program Files\\SYSTAT 10\\;C:\\Program 
>>> Files\\SYSTAT 10\\XGRAPH\\;C:\\Program Files\\Wave Systems Corp\\Dell 
>>> Preboot Manager\\Access Client\\v5\\;C:\\Program Files\\ATI 
>>> Technologies\\ATI.ACE\\Core-Static;c:\\Program Files\\Microsoft SQL 
>>> Server\\90\\Tools\\binn\\"
>>>> 
>>>> Thank you
>>>> 
>>>> Felipe D. Carrillo  Supervisory Fishery Biologist  Department of the 
>>>> Interior  US Fish & Wildlife Service  California, USA
>>>> 
>>>> 
>>>> --- On Thu, 10/16/08, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
>>>> 
>>>>> Try running it as texi2dvi("Sweave-test-1.tex",
>>>>> pdf=TRUE, quiet=FALSE), and post the list of error messages.
>>>>> 
>>>>> You should also show us the results of sessionInfo() and 
>>>>> Sys.getenv("PATH"), and tell us which version of
>>>>> LaTeX you have installed.
>>>>> 
>>>>> Duncan Murdoch
>>>>> > > ______________________________________________
>>>>> > R-help at r-project.org mailing list
>>>>> > https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> > PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> > and provide commented, minimal, self-contained,
>>>>> reproducible code.
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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

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