Whatever we choose, we should discourage the use of other fonts: one of the
advantages of bioc style is to make it easy to compiler on other computers.
 Fonts can be hard to deal with on some tex systems, especially if you
don't have root access.  Having a "nice" font is not worth the added
complexity of this.  And I also agree that the font (whatever is chosen)
should be the same for knitr and Sweave.

Best,
Kasper


On Wed, Mar 12, 2014 at 12:40 PM, Laurent Gatto <lg390@cam.ac.uk> wrote:

>
> > 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 <mtmorgan@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
> >>
> >>
> >> _______________________________________________
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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