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?
Thank you very much in advance.
Best wishes,
Laurent
[Bioc-devel] BiocStyle and fonts
10 messages · Martin Morgan, Andrzej Oleś, Kasper Daniel Hansen +1 more
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 at 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
[...]
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).
[...]
Not really sure where that takes us; the helvetica fonts look better IMO.
Thanks for the clarifications, Martin. Might be worth documenting this in the vignette. I'm personally not too keen on the helvetica font. Best wishes, Laurent
Martin
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 <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
_______________________________________________ Bioc-devel at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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
_______________________________________________ Bioc-devel at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20140312/74a13868/attachment.pl>
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
_______________________________________________ Bioc-devel at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Should we then just drop \RequirePackage{helvet} from BiocStyle?
That seems a reasonable solution to me. Laurent
Cheers, Andrzej
On 03/12/2014 08:18 AM, Laurent Gatto wrote:
Should we then just drop \RequirePackage{helvet} from BiocStyle?
That seems a reasonable solution to me.
yep! Martin
Laurent
Cheers, Andrzej
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
Done!
On Wed, Mar 12, 2014 at 5:01 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
On 03/12/2014 08:18 AM, Laurent Gatto wrote:
Should we then just drop \RequirePackage{helvet} from BiocStyle?
That seems a reasonable solution to me.
yep! Martin
Laurent
Cheers, Andrzej
-- 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