Sexpr not getting expanded in Sweave
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 ?test.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