[R] Resolved: Problem in local ~/.fonts.conf broke symbol font in pdf device (Was: Re: Plotmath, sweave and lattice graphics interaction problem)
Gavin Simpson
gavin.simpson at ucl.ac.uk
Sat Aug 29 11:42:32 CEST 2009
On Sat, 2009-08-29 at 09:04 +1000, Duncan Mackay wrote:
> Hi Gavin
>
> I am running on windows and have no problem
Thanks for confirming that this appears to be peculiar to my system,
Duncan. I've narrowed this down to just the PDF device so nothing to do
with Sweave and / or lattice as the characters are missing with base
graphics also.
I suspect a font issue somewhere on my system. In fact I've just found
the source of the problem now. Under earlier versions of Fedora (9 and
10) I had to use the following ~/.fonts.conf
<alias binding="same">
<family>ZapfDingbats</family>
<accept><family>Dingbats</family></accept>
<family>Symbol</family>
<accept><family>Standard Symbols L</family></accept>
</alias>
The definition for Symbol is what is breaking this font for me on the
pdf device. The suggestion for ~/.fonts.conf in ?pdf,
<alias binding="same">
<family>ZapfDingbats</family>
<accept><family>Dingbats</family></accept>
</alias>
solves the problem with the symbol font on Fedora 11 for me but still
fixes the pch = 1 issue.
All the best,
Gavin
>
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] datasets utils stats graphics grDevices
> grid methods base
>
> other attached packages:
> [1] Hmisc_3.6-1 R.oo_1.4.8 R.methodsS3_1.0.3
> foreign_0.8-37 chron_2.3-30 MASS_7.2-48 lattice_0.17-25
>
> loaded via a namespace (and not attached):
> [1] cluster_1.12.0
>
> Can forward you my sweave file et al if required
>
> Regards
>
> Duncan Mackay
> Department of Agronomy and Soil Science
> University of New England
> ARMIDALE NSW 2351
> Email home: mackay at northnet.com.au
>
> At 03:10 29/08/2009, you wrote:
> >Dear List,
> >
> >I have hit this problem with using a plotmath expression in an axis
> >label on a lattice plot I'm including in a Sweave document. The actual
> >document is far too long and boring (unless you are interested in the
> >hydrochemistry of upland lakes) to include here, but the following
> >minimal example reproduces the problem; basically, the PDF produced by
> >Sweave has missing characters in the plotmath label whilst the eps file
> >doesn't.
> >
> >Here is the minimal Rnw document:
> >
> >\documentclass[a4paper,12pt]{article}
> >\usepackage{graphicx,xspace}
> >\usepackage[utf8]{inputenc}
> >\usepackage[left=1.5cm,top=2cm,bottom=2cm,right=1.5cm]{geometry}
> >
> >\usepackage{/home/gavin/R/2.9-patched/build/share/texmf/Sweave}
> >\setkeys{Gin}{width=1\textwidth}
> >
> >\begin{document}
> >\title{FOO}
> >\author{Gavin Simpson}
> >
> >\maketitle
> >
> ><<fig=true>>=
> >require(lattice)
> >dat <- data.frame(A = runif(10), B = runif(10))
> >print(xyplot(A ~ B, data = dat,
> > ylab = expression(H^"+" ~ (mu*eq ~ L^"-1"))))
> >@
> >
> >\end{document}
> >
> >Note the ylab expression:
> >
> >ylab = expression(H^"+" ~ (mu*eq ~ L^"-1"))
> >
> >this produces a ylab like H+ (mueq L-1) when run interactively and on
> >the eps file, but the pdf file is missing the parentheses and the mu
> >(micro) symbol.
> >
> >R session info:
> >
> > > sessionInfo()
> >R version 2.9.1 Patched (2009-08-07 r49104)
> >x86_64-unknown-linux-gnu
> >
> >locale:
> >LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> >
> >attached base packages:
> >[1] tools stats graphics grDevices utils datasets
> >methods
> >[8] base
> >
> >other attached packages:
> >[1] lattice_0.17-25
> >
> >loaded via a namespace (and not attached):
> >[1] grid_2.9.1
> >
> >So I'm running this in a UTF-8 locale. Is it this that is causing the
> >problem? Any suggestions as to how to proceed?
> >
> >Thanks in advance,
> >
> >G
> >
> >--
> >%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> > Dr. Gavin Simpson [t] +44 (0)20 7679 0522
> > ECRC, UCL Geography, [f] +44 (0)20 7679 0565
> > Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
> > Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
> > UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
> >%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> >
> >______________________________________________
> >R-help at r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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