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

[Nicolas Delhomme]

Hej Martin!

On 11 Dec 2013, at 12:19, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> 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.

Thanks, I came up with a \biocComment of my own :-), so it won’t be much change to adapt.

> 
> 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?

I’m afraid my tex knowledge is not good enough to answer that. And my google-fu appears poor today.

Anyway, thanks for the fix!

Nico

> 
> 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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