> 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.
Definitely. The difference in fonts is what prompted my enquiry in the
first place, not the choice of font per se.
Best wishes,
Laurent
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>>
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