Hi Laurent, Martin,
thank you for bringing this up! As pointed out by Martin, currently
the 'helvet' package gets overridden by Sweave, so this setting
affects only the knitr output.
My feeling is that the default font style should be the same
regardless of the engine used. Too keep thing simple, I would suggest
removing from Bioconductor.sty the following line forcing a particular
font:
\RequirePackage{helvet}
It doesn't help in case of Sweave documents anyway, and setting a
different font in knitr (e.g. helvetica) is straightforward and can be
done manually by simply adding \usepackage{helvet} to the vignette
source if desired.
When it comes to font styles, that's of course a matter of taste and I
don't want to start a war here. However, I think the Latex already
provides a decent default sans serif font and there is no particular
need for BiocStyle to override it.
Cheers,
Andrzej
On Wed, Mar 12, 2014 at 1:58 AM, Martin Morgan <mtmor...@fhcrc.org> wrote:
> On 03/11/2014 10:38 AM, Laurent Gatto wrote:
>>
>>
>> Dear all,
>>
>> Compiling the following with Sweave
>>
>> \documentclass{article}
>> <<style, eval=TRUE, echo=FALSE, results=tex>>=
>> BiocStyle::latex()
>> @
>> \bioctitle{Hello world}
>> \begin{document}
>> \maketitle
>> \section{Section}
>> Some text
>> <<pxdata>>=
>> print("Hello world")
>> @
>> \end{document}
>>
>> $ R CMD Sweave --engine=utils::Sweave --pdf test.Rnw
>>
>> and this one with knitr
>>
>> \documentclass{article}
>> <<style, eval=TRUE, echo=FALSE, results='asis'>>=
>> BiocStyle::latex()
>> @
>> \bioctitle{Hello world}
>> \begin{document}
>> \maketitle
>> \section{Section}
>> Some text
>> <<pxdata>>=
>> print("Hello world")
>> @
>> \end{document}
>>
>> $R CMD Sweave --engine=knitr::knitr --pdf test.Rnw
>>
>> produces two pdf documents with different fonts.
>>
>> As a positive control, using the two engines without BiocStyle result in
>> pdf files with identical fonts.
>>
>> Is this a documented side effect of BiocStyle?
>
>
> Hi Laurent --
>
> Here's a latex document to play with, via R CMD Sweave --pdf test.Rnw
>
> \documentclass{article}
> \usepackage{helvet}
> \renewcommand{\familydefault}{\sfdefault}
> \usepackage[noae]{Sweave}
>
> \title{Hello world}
> \begin{document}
> \maketitle
> \section{Section}
> Some text
> \end{document}
>
> Seems like an interaction between the 'helvet' package (used by BiocStyle)
> and the 'ae' package (used by Sweave). Get knitr-like output with either
> \usepackage[noae]{Sweave} or by placing \usepackage{Sweave} before
> \usepackage{helvet} (i.e., before the BiocStyle() chunk).
>
> I think the ae package forces use of sans serif computer modern fonts, which
> you can 'see' from the output of pdflatex test.tex with ae
>
> ...
>
> [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./sweave.aux)
> )</usr/sh
> are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/share/te
> xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss12.pfb></usr/share/texlive/
> texmf-dist/fonts/type1/public/amsfonts/cm/cmss17.pfb></usr/share/texlive/texmf-
> dist/fonts/type1/public/amsfonts/cm/cmssbx10.pfb>
>
> versus without
>
> [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./sweave.aux)
> ){/usr/sh
> are/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-di
> st/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/fonts/typ
> e1/urw/helvetic/uhvr8a.pfb>
>
> Not really sure where that takes us; the helvetica fonts look better IMO.
>
> Martin
>
>
>>
>> Thank you very much in advance.
>>
>> Best wishes,
>>
>> Laurent
>>
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>>
>
>
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