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
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