R help - Nov 2010 - Troubleshooting sweave

Hi All,

I've reproduced the example from Prof. Friedrich Leisch's webpage. When
I
write sweave("Example-1.Snw") OR sweave("Example-1.Rnw"),
(yes, I renamed
them). I get the following error:

Writing to file example-1.tex
Processing code chunks ...
 1 : echo term verbatim

Error:  chunk 1
Error in library(ctest) : there is no package called 'ctest'

Also while I'm at it, is there an R command to compile the tex file as a
pdf or does the Sweave() function do that for me?

Thanks,
Sachin
p.s. sorry about the corporate notice.

example-1.Rnw: from http://www.statistik.lmu.de/~leisch/Sweave/

\documentclass[a4paper]{article}

\title{Sweave Example 1}
\author{Friedrich Leisch}

\begin{document}

\maketitle

In this example we embed parts of the examples from the
\texttt{kruskal.test} help page into a \LaTeX{} document:

<<>>data(airquality)
library(ctest)
kruskal.test(Ozone ~ Month, data = airquality)
@
which shows that the location parameter of the Ozone
distribution varies significantly from month to month. Finally we
include a boxplot of the data:

\begin{center}
<<fig=TRUE,echo=FALSE>>boxplot(Ozone ~ Month, data = airquality)
@
\end{center}

\end{document}

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On Nov 11, 2010, at 5:42 PM, sachinthaka.abeywardana at allianz.com.au wrote:
> 
> Hi All,
> 
> I've reproduced the example from Prof. Friedrich Leisch's webpage.
When I
> write sweave("Example-1.Snw") OR
sweave("Example-1.Rnw"), (yes, I renamed
> them). I get the following error:
> 
> Writing to file example-1.tex
> Processing code chunks ...
> 1 : echo term verbatim
> 
> Error:  chunk 1
> Error in library(ctest) : there is no package called 'ctest'
> 
> Also while I'm at it, is there an R command to compile the tex file as
a
> pdf or does the Sweave() function do that for me?
> 
> Thanks,
> Sachin
> p.s. sorry about the corporate notice.
> 
> example-1.Rnw: from http://www.statistik.lmu.de/~leisch/Sweave/
> 
> \documentclass[a4paper]{article}
> 
> \title{Sweave Example 1}
> \author{Friedrich Leisch}
> 
> \begin{document}
> 
> \maketitle
> 
> In this example we embed parts of the examples from the
> \texttt{kruskal.test} help page into a \LaTeX{} document:
> 
> <<>>> data(airquality)
> library(ctest)
> kruskal.test(Ozone ~ Month, data = airquality)
> @
> which shows that the location parameter of the Ozone
> distribution varies significantly from month to month. Finally we
> include a boxplot of the data:
> 
> \begin{center}
> <<fig=TRUE,echo=FALSE>>> boxplot(Ozone ~ Month, data =
airquality)
> @
> \end{center}
> 
> \end{document}

'ctest' was a package that was merged into the 'stats' package
in R version 1.9.0, which was released back in 2004. So it would appear that
Fritz (cc'd here) has not updated the examples to reflect that change.

A simple fix would be to remove the 'library(ctest)' line from the file.

If you look at:

  require(utils)
  ?Sweave

there are some examples of using both internal and external R commands to
process the file into a PDF. Sweave itself just generates the TeX source file
(.tex), which then requires a LaTeX installation to process that file into the
PDF (or EPS as may be required).

I would also be sure to review ?RweaveLatex for more information, including some
potential environment issues that you may have to address in the Details
section. Fritz' Sweave FAQ and manual on his site are also good references
as may be required.

Presuming that you have LaTeX installed on your computer, the easiest thing to
do may to use:

  pdflatex YourFileName.tex

at the command line, to process the resultant TeX file into a PDF. The steps can
be a bit more complicated if you are using any LaTeX packages that might require
the intermediate creation of a DVI and PS file. That would include packages such
as PSTricks, etc.

HTH,

Marc Schwartz

On 11/11/2010 3:42 PM, sachinthaka.abeywardana at allianz.com.au
wrote:
>
> Hi All,
>
> I've reproduced the example from Prof. Friedrich Leisch's webpage.
When I
> write sweave("Example-1.Snw") OR
sweave("Example-1.Rnw"), (yes, I renamed
> them). I get the following error:
>
> Writing to file example-1.tex
> Processing code chunks ...
>   1 : echo term verbatim
>
> Error:  chunk 1
> Error in library(ctest) : there is no package called 'ctest'
That error message indicates that you attempted to load a package 
('ctest') that is not installed.  Normally, you would just need to 
install the package using the install.package() command. However, there 
is (no longer) a ctest package to install.  Digging through the email 
archives, it appears to have been merged into the stats package back in 
version 1.9.0.  So you can just delete the "library(ctest)" line in
the
Rnw file.

You can search for examples that are more recent; this one must have 
been from before April 2004 (when R 1.9.0 was released).  Though I don't 
blame you for being confused; I would also have expected the examples on 
what seems to be the canonical homepage to work and not be out-of-date.
> Also while I'm at it, is there an R command to compile the tex file as
a
> pdf or does the Sweave() function do that for me?
Check out the texi2dvi() function in the tools package.  If you want a 
PDF, be sure to use the pdf option.
> Thanks,
> Sachin
> p.s. sorry about the corporate notice.
>
> example-1.Rnw: from http://www.statistik.lmu.de/~leisch/Sweave/
>
> \documentclass[a4paper]{article}
>
> \title{Sweave Example 1}
> \author{Friedrich Leisch}
>
> \begin{document}
>
> \maketitle
>
> In this example we embed parts of the examples from the
> \texttt{kruskal.test} help page into a \LaTeX{} document:
>
> <<>>> data(airquality)
> library(ctest)
> kruskal.test(Ozone ~ Month, data = airquality)
> @
> which shows that the location parameter of the Ozone
> distribution varies significantly from month to month. Finally we
> include a boxplot of the data:
>
> \begin{center}
> <<fig=TRUE,echo=FALSE>>> boxplot(Ozone ~ Month, data =
airquality)
> @
> \end{center}
>
> \end{document}
-- 
Brian S. Diggs, PhD
Senior Research Associate, Department of Surgery
Oregon Health & Science University

sachinthaka.abeywardana at allianz.com.au wrote:
> Hi All,
> 
> I've reproduced the example from Prof. Friedrich Leisch's webpage.
When I
> write sweave("Example-1.Snw") OR
sweave("Example-1.Rnw"), (yes, I renamed
> them). I get the following error:
> 
> Writing to file example-1.tex
> Processing code chunks ...
>  1 : echo term verbatim
> 
> Error:  chunk 1
> Error in library(ctest) : there is no package called 'ctest'
> 
> Also while I'm at it, is there an R command to compile the tex file as
a
> pdf or does the Sweave() function do that for me?
The patchDVI package on R-forge includes functions to process (possibly 
multiple) Sweave inputs into .pdf or .dvi files.

E.g.

SweavePDF("Example.Rnw")


Duncan Murdoch
> 
> Thanks,
> Sachin
> p.s. sorry about the corporate notice.
> 
> example-1.Rnw: from http://www.statistik.lmu.de/~leisch/Sweave/
> 
> \documentclass[a4paper]{article}
> 
> \title{Sweave Example 1}
> \author{Friedrich Leisch}
> 
> \begin{document}
> 
> \maketitle
> 
> In this example we embed parts of the examples from the
> \texttt{kruskal.test} help page into a \LaTeX{} document:
> 
> <<>>> data(airquality)
> library(ctest)
> kruskal.test(Ozone ~ Month, data = airquality)
> @
> which shows that the location parameter of the Ozone
> distribution varies significantly from month to month. Finally we
> include a boxplot of the data:
> 
> \begin{center}
> <<fig=TRUE,echo=FALSE>>> boxplot(Ozone ~ Month, data =
airquality)
> @
> \end{center}
> 
> \end{document}
> 
> --- Please consider the environment before printing this email --- 
> 
> Allianz - Best General Insurance Company of the Year 2010*
> Allianz - General Insurance Company of the Year 2009+ 
> 
> * Australian Banking and Finance Insurance Awards
> + Australia and New Zealand Insurance Industry Awards 
> 
> This email and any attachments has been sent by Allianz Australia Insurance
Limited (ABN 15 000 122 850) and is intended solely for the addressee. It is
confidential, may contain personal information and may be subject to legal
professional privilege. Unauthorised use is strictly prohibited and may be
unlawful. If you have received this by mistake, confidentiality and any legal
privilege are not waived or lost and we ask that you contact the sender and
delete and destroy this and any other copies. In relation to any legal use you
may make of the contents of this email, you must ensure that you comply with the
Privacy Act (Cth) 1988 and you should note that the contents may be subject to
copyright and therefore may not be reproduced, communicated or adapted without
the express consent of the owner of the copyright.
> Allianz will not be liable in connection with any data corruption,
interruption, delay, computer virus or unauthorised access or amendment to the
contents of this email. If this email is a commercial electronic message and you
would prefer not to receive further commercial electronic messages from Allianz,
please forward a copy of this email to unsubscribe at allianz.com.au with the
word unsubscribe in the subject header.
> 
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

seems like the texi2dvi doesnt exist on R2.12.0 anymore?

Sachin
p.s. sorry about corporate notice

--- Please consider the environment before printing this email --- 

Allianz - Best General Insurance Company of the Year 2010*
Allianz - General Insurance Company of the Year 2009+ 

* Australian Banking and Finance Insurance Awards
+ Australia and New Zealand Insurance Industry Awards 

This email and any attachments has been sent by Allianz Australia Insurance
Limited (ABN 15 000 122 850) and is intended solely for the addressee. It is
confidential, may contain personal information and may be subject to legal
professional privilege. Unauthorised use is strictly prohibited and may be
unlawful. If you have received this by mistake, confidentiality and any legal
privilege are not waived or lost and we ask that you contact the sender and
delete and destroy this and any other copies. In relation to any legal use you
may make of the contents of this email, you must ensure that you comply with the
Privacy Act (Cth) 1988 and you should note that the contents may be subject to
copyright and therefore may not be reproduced, communicated or adapted without
the express consent of the owner of the copyright.
Allianz will not be liable in connection with any data corruption, interruption,
delay, computer virus or unauthorised access or amendment to the contents of
this email. If this email is a commercial electronic message and you would
prefer not to receive further commercial electronic messages from Allianz,
please forward a copy of this email to unsubscribe at allianz.com.au with the
word unsubscribe in the subject header.