[Bioc-devel] Conflict between BiocStyle and the verbatim package

On 12/03/2013 12:50 PM, Martin Morgan wrote:

On 12/03/2013 12:30 PM, Nicolas Delhomme wrote:

Hej Martin!

I?d like to have multi-line comments in my vignette and the easiest way I know
is to use the ?comment? environment from the verbatim package - i.e.
\begin{comment}?\end{comment}. However, when I do this, i.e. load the verbatim
package after having ?sourced? the BiocStyle package, generating the pdf just
fails without any error message.

Hi Nico -- I addressed this by changing BiocStyle to define the function 
\bioccomment rather than \comment, so there is no conflict with verbatim.

Other name mangling might be necessary to avoid conflicts with other styles -- 
\email, \file, \fixme, \warning -- but I wonder if there is some other solution?

Martin

Here?s a tiny .Rnw example of how to reproduce the error:

\documentclass[11pt,a4paper]{article}
% Bioc style
<<style, eval=TRUE, echo=FALSE, results=tex>>=
BiocStyle::latex()
@
\usepackage{verbatim}
\begin{document}
Some text
\begin{comment}
some comments not to be seen by the user
\end{comment}
Some more text
\end{document}

The generated pdf stops after the text ?Some text?. I tried to track it down,
but I?m out of my depth in latex style file. Do you have any idea what is
happening? And do you have any suggestion of how I could go around this other
than using % on every comment line?

If I take your file and

  R CMD Sweave Nico.Rnw
  pdflatex Nico.tex

I get

! Undefined control sequence.
\f at ncyolh ->\thetitle
                      \strut
l.15 \end{document}

?

which is because the vignette needs to have a title, e.g., in the preamble

\usepackage{verbatim}
\title{My amazing document}
\begin{document}

If I add this, then things seem to work fine.

The undefined control sequence doesn't sound like what you saw, so maybe more
details are needed? I'm using

$ R --vanilla --slave -e "R.version.string"
[1] "R Under development (unstable) (2013-12-01 r64371)"

$ pdflatex --version
pdfTeX 3.1415926-1.40.10-2.2 (TeX Live 2009/Debian)

Martin

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Ume? Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? S-901 87 Sweden

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