[R] Sexpr not getting expanded in Sweave

[Marc Schwartz]

On Feb 23, 2012, at 5:22 PM, Michael Kubovy wrote:

> An Sweave file, 'test.Rnw':
> 
> \documentclass{article}
> \title{Sweave minimal}
> \author{MK}
> \begin{document}
> \maketitle
> We try Sweave:
> <<1>>=
> data(airquality)
> summary(airquality)
> x <- airquality[1, 1]
> @
> 
> I try Sexpr: \Sexpr{x}
> 
> We plot:
> \begin{center}
> <<2, fig=TRUE, echo=FALSE >>=
> boxplot(Ozone ~ Month, data = airquality) 
> @
> \end{center}
> \end{document}
> 
> I check the sessionInfo:
> 
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] datasets  splines   utils     stats     graphics  grDevices methods   base     
> 
> other attached packages:
> [1] cacheSweave_0.6     stashR_0.3-4        filehash_2.2        concord_1.4-9       irr_0.83            lpSolve_5.6.6       ca_0.33             rgl_0.92.798       
> [9] vegan_2.0-2         permute_0.6-3       reshape_0.8.4       plyr_1.7.1          ggplot2_0.9.0       doBy_4.5.2          snow_0.3-8          lme4_0.999375-42   
> [17] Matrix_1.0-3        lattice_0.20-0      multcomp_1.2-10     mvtnorm_0.9-9992    R2HTML_2.2          BiocInstaller_1.2.1 ctv_0.7-4           sos_1.3-1         
> [25] brew_1.0-6          Hmisc_3.9-2         survival_2.36-12    MASS_7.3-17        
> 
> loaded via a namespace (and not attached):
> [1] car_2.0-12         cluster_1.14.2     colorspace_1.1-1   dichromat_1.2-4    digest_0.5.1       grid_2.14.1        memoise_0.1        munsell_0.3        nlme_3.1-103      
> [10] proto_0.3-9.2      RColorBrewer_1.0-5 reshape2_1.2.1     scales_0.1.0       stats4_2.14.1      stringr_0.6        tools_2.14.1      
> 
> and run Sweave:
> 
>> Sweave(file = 'test.Rnw')
> Writing to file test.tex
> Processing code chunks with options ...
> 1 : echo keep.source term verbatim (label = 1)
> 2 : keep.source term verbatim pdf  (label = 2)
> 
> You can now run (pdf)latex on Œtest.tex‚
> 
> It works as it should except for \Sexpr
> 
> \documentclass{article}
> \title{Sweave minimmal}
> \author{MK}
> \usepackage{Sweave}
> \begin{document}
> \maketitle
> We try Sweave:
> \begin{Schunk}
> \begin{Sinput}
>> data(airquality)
>> summary(airquality)
> \end{Sinput}
> \begin{Soutput}
>     Ozone          Solar.R         Wind            Temp          Month           Day      
> Min.   :  1.0   Min.   :  7   Min.   : 1.70   Min.   :56.0   Min.   :5.00   Min.   : 1.0  
> 1st Qu.: 18.0   1st Qu.:116   1st Qu.: 7.40   1st Qu.:72.0   1st Qu.:6.00   1st Qu.: 8.0  
> Median : 31.5   Median :205   Median : 9.70   Median :79.0   Median :7.00   Median :16.0  
> Mean   : 42.1   Mean   :186   Mean   : 9.96   Mean   :77.9   Mean   :6.99   Mean   :15.8  
> 3rd Qu.: 63.2   3rd Qu.:259   3rd Qu.:11.50   3rd Qu.:85.0   3rd Qu.:8.00   3rd Qu.:23.0  
> Max.   :168.0   Max.   :334   Max.   :20.70   Max.   :97.0   Max.   :9.00   Max.   :31.0  
> NA's   : 37.0   NA's   :  7                                                               
> \end{Soutput}
> \begin{Sinput}
>> x <- airquality[1, 1]
> \end{Sinput}
> \end{Schunk}
> 
> We try Sexpr: \Sexpr{x}
> 
> We plot:
> \begin{center}
> \includegraphics{test-2}
> \end{center}
> \end{document}
> 
> The beginning of the .log file:
> This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011) (format=pdflatex 2012.2.4)  23 FEB 2012 18:19
> entering extended mode
> \write18 enabled.
> %&-line parsing enabled.
> **test.tex
> (./test.tex
> LaTeX2e <2011/06/27>
> 
> Any thought? Please CC me when replying.
> 
> Michael Kubovy


There have been problems reported over the years on this due to a conflict with the R2HTML package, which you have loaded as indicated above. If you can run your session without that package, try that. Otherwise use:

  options(SweaveSyntax = "SweaveSyntaxNoweb")
  Sweave("test.Rnw")

or

  Sweave("test.Rnw", syntax = "SweaveSyntaxNoweb")

This is in the Sweave FAQ and Manual.

HTH,

Marc Schwartz