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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