R help - Feb 2008 - Sweave produces gibberish instead of apostrophe in pdf

Dear All,

I try to use Sweave to make a document. But when I use the Sweave() 
command on it and build a pdf with pdflatex (3.141592-1.40.3) my 
apostrophes are replaced by some gibberish (an 'a' with a hat on it, a 
capital A with a arc pointing upwards on it and a capital Y with two 
points on it). If I manually replace the apostrophes using the keyboard, 
I get a different looking apostrophe and the output is correct.

I'm using Debian Linux (Lenny) with TexLive, Kile and R 2.6.1.

This is a sample, the problem is in the lm output in the "Signif.
codes"
line:

\documentclass[a4paper,10pt]{article}
\title{Spam}
\author{F. Bar}

\begin{document}
<<reg>>n <- 50
x <- seq(1, n)
a.true <- 3
b.true <- 1.5
y.true <- a.true + b.true * x
s.true <- 17.3
y <- y.true + s.true * rnorm(n)
out1 <- lm(y ~ x)
summary(out1)
@
\end{document}

And the resulting .tex file:

\documentclass[a4paper,10pt]{article}
\title{Spam}
\author{F. Bar}

\usepackage{Sweave}
\begin{document}
\begin{Schunk}
\begin{Sinput}
 > n <- 50
 > x <- seq(1, n)
 > a.true <- 3
 > b.true <- 1.5
 > y.true <- a.true + b.true * x
 > s.true <- 17.3
 > y <- y.true + s.true * rnorm(n)
 > out1 <- lm(y ~ x)
 > summary(out1)
\end{Sinput}
\begin{Soutput}
Call:
lm(formula = y ~ x)

Residuals:
Min 1Q Median 3Q Max
-31.9565 -9.4745 -0.1708 7.3759 44.6538

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.07386 4.64712 -0.016 0.987
x 1.57405 0.15860 9.924 3.25e-13 ***
---
Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 .? 0.1 ? ? 1

Residual standard error: 16.18 on 48 degrees of freedom
Multiple R-Squared: 0.6723, Adjusted R-squared: 0.6655
F-statistic: 98.49 on 1 and 48 DF, p-value: 3.245e-13
\end{Soutput}
\end{Schunk}
\end{document}

cheers and thanks for any help,
Paul

-- 
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: 	+31302535773
Fax:	+31302531145
http://intamap.geo.uu.nl/~paul

On Wed, 2008-02-27 at 11:35 +0100, Paul Hiemstra wrote:
> Dear All,
> 
> I try to use Sweave to make a document. But when I use the Sweave() 
> command on it and build a pdf with pdflatex (3.141592-1.40.3) my 
> apostrophes are replaced by some gibberish (an 'a' with a hat on
it, a
> capital A with a arc pointing upwards on it and a capital Y with two 
> points on it). If I manually replace the apostrophes using the keyboard, 
> I get a different looking apostrophe and the output is correct.
> 
> I'm using Debian Linux (Lenny) with TexLive, Kile and R 2.6.1.
I presume that R is running in a UTF-8 locale on your Debian box (or
some other locale that is different to the one pdflatex is working in);
the fancy quotes used in some print methods in R aren't available in all
locale/font encodings and these get interpreted as the "gibberish" you
are seeing.

Stick this in your preamble and see if it works (you might need to
install a TexLive package from your usual Debian repository to get this
[LaTeX] package installed):

\usepackage[utf8x]{inputenc}

it did for me on my Fedora box when I first came across this issue.

HTH

G
> 
> This is a sample, the problem is in the lm output in the "Signif.
codes"
> line:
> 
> \documentclass[a4paper,10pt]{article}
> \title{Spam}
> \author{F. Bar}
> 
> \begin{document}
> <<reg>>> n <- 50
> x <- seq(1, n)
> a.true <- 3
> b.true <- 1.5
> y.true <- a.true + b.true * x
> s.true <- 17.3
> y <- y.true + s.true * rnorm(n)
> out1 <- lm(y ~ x)
> summary(out1)
> @
> \end{document}
> 
> And the resulting .tex file:
> 
> \documentclass[a4paper,10pt]{article}
> \title{Spam}
> \author{F. Bar}
> 
> \usepackage{Sweave}
> \begin{document}
> \begin{Schunk}
> \begin{Sinput}
>  > n <- 50
>  > x <- seq(1, n)
>  > a.true <- 3
>  > b.true <- 1.5
>  > y.true <- a.true + b.true * x
>  > s.true <- 17.3
>  > y <- y.true + s.true * rnorm(n)
>  > out1 <- lm(y ~ x)
>  > summary(out1)
> \end{Sinput}
> \begin{Soutput}
> Call:
> lm(formula = y ~ x)
> 
> Residuals:
> Min 1Q Median 3Q Max
> -31.9565 -9.4745 -0.1708 7.3759 44.6538
> 
> Coefficients:
> Estimate Std. Error t value Pr(>|t|)
> (Intercept) -0.07386 4.64712 -0.016 0.987
> x 1.57405 0.15860 9.924 3.25e-13 ***
> ---
> Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 .? 0.1 ? ? 1
> 
> Residual standard error: 16.18 on 48 degrees of freedom
> Multiple R-Squared: 0.6723, Adjusted R-squared: 0.6655
> F-statistic: 98.49 on 1 and 48 DF, p-value: 3.245e-13
> \end{Soutput}
> \end{Schunk}
> \end{document}
> 
> cheers and thanks for any help,
> Paul
> 
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

These are not 'apostrophe's: it's (that is an apostrophe) misleading
to
call them that.  They are single quotes, and there are two sorts if you 
look carefully.

Probably you are using a UTF-8 locale and not telling LaTeX (or us) so. 
There are several ways to do so, depending on the age of your LaTeX setup.

\usepackage[utf8]{inputenc}

is one.

Alternatively, you can tell R not to use UTF-8 quotes with 
options(useFancyQuotes=FALSE).

Please note the 'at a minimum' information the posting guide asked you 
for -- it included the locale.


On Wed, 27 Feb 2008, Paul Hiemstra wrote:
> Dear All,
>
> I try to use Sweave to make a document. But when I use the Sweave()
> command on it and build a pdf with pdflatex (3.141592-1.40.3) my
> apostrophes are replaced by some gibberish (an 'a' with a hat on
it, a
> capital A with a arc pointing upwards on it and a capital Y with two
> points on it). If I manually replace the apostrophes using the keyboard,
> I get a different looking apostrophe and the output is correct.
>
> I'm using Debian Linux (Lenny) with TexLive, Kile and R 2.6.1.
>
> This is a sample, the problem is in the lm output in the "Signif.
codes"
> line:
>
> \documentclass[a4paper,10pt]{article}
> \title{Spam}
> \author{F. Bar}
>
> \begin{document}
> <<reg>>> n <- 50
> x <- seq(1, n)
> a.true <- 3
> b.true <- 1.5
> y.true <- a.true + b.true * x
> s.true <- 17.3
> y <- y.true + s.true * rnorm(n)
> out1 <- lm(y ~ x)
> summary(out1)
> @
> \end{document}
>
> And the resulting .tex file:
>
> \documentclass[a4paper,10pt]{article}
> \title{Spam}
> \author{F. Bar}
>
> \usepackage{Sweave}
> \begin{document}
> \begin{Schunk}
> \begin{Sinput}
> > n <- 50
> > x <- seq(1, n)
> > a.true <- 3
> > b.true <- 1.5
> > y.true <- a.true + b.true * x
> > s.true <- 17.3
> > y <- y.true + s.true * rnorm(n)
> > out1 <- lm(y ~ x)
> > summary(out1)
> \end{Sinput}
> \begin{Soutput}
> Call:
> lm(formula = y ~ x)
>
> Residuals:
> Min 1Q Median 3Q Max
> -31.9565 -9.4745 -0.1708 7.3759 44.6538
>
> Coefficients:
> Estimate Std. Error t value Pr(>|t|)
> (Intercept) -0.07386 4.64712 -0.016 0.987
> x 1.57405 0.15860 9.924 3.25e-13 ***
> ---
> Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 .? 0.1 ? ? 1
>
> Residual standard error: 16.18 on 48 degrees of freedom
> Multiple R-Squared: 0.6723, Adjusted R-squared: 0.6655
> F-statistic: 98.49 on 1 and 48 DF, p-value: 3.245e-13
> \end{Soutput}
> \end{Schunk}
> \end{document}
>
> cheers and thanks for any help,
> Paul
>
> --
> Drs. Paul Hiemstra
> Department of Physical Geography
> Faculty of Geosciences
> University of Utrecht
> Heidelberglaan 2
> P.O. Box 80.115
> 3508 TC Utrecht
> Phone: 	+31302535773
> Fax:	+31302531145
> http://intamap.geo.uu.nl/~paul
>
> ______________________________________________
> 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