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

[Martin Morgan]

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
>> Umeå Plant Science Center
>>
>> Tel: +46 90 786 7989
>> Email: nicolas.delhomme at umu.se
>> SLU - Umeå universitet
>> Umeå S-901 87 Sweden
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>


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