[Bioc-devel] BiocStyle and fonts

[Andrzej Oleś]

Should we then just drop \RequirePackage{helvet} from BiocStyle?

Cheers,
Andrzej

On Wed, Mar 12, 2014 at 3:27 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> 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 at 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 at 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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>> >>
>> >>
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