[R] svg malformed on CentOS (epel R)

[Paul Murrell]

Hi

On 14/03/2011 2:30 p.m., Jeroen Ooms wrote:
> There is an issue with the default svg device on a centos workstation that I
> am using. It does not result in an error, but it produces malformed svg
> images. Exactly the same script works just fine on an ubuntu box. On Ubuntu
> I am using R binary that comes with maverick, on centos I am using the
> latest R binary from EPEL. Other than that both boxes are pretty clean, with
> only the dependencies installed that are automatically installed when
> installing R.
>
> For example a testscript like this
> svg("plot.svg");
> plot(cars);
> dev.off();
>
> should produce this: http://www.stat.ucla.edu/~jeroen/files/plot_good.svg
> (ubuntu), but on centos it produces this:
> http://www.stat.ucla.edu/~jeroen/files/plot_bad.svg.
>
> It looks very much as if there is something wrong with the fronts; maybe I
> am missing some library. However, as this is a production server, I don't
> want to go install random packages to see if this fixes the problem.
>
> Some questions:
>
> - How could I fix it?
> - Why is R not throwing an error instead of producing a malformed plot?
> - Maybe we could notify the R binary maintainers from fedora to add a formal
> dependency so that it works 'out of the box'?

Looking at the raw SVG, the letter glyphs are all defined at the top and 
one difference between the files is the presence of the 'overflow' 
attribute in plot_good.svg.  You can manually edit the file to add this 
attribute to plot_bad.svg and the text becomes visible.  So this is a 
clipping problem within the SVG that is being generated.  My guess is 
that this is due to a difference in version of the Cairo library, but 
that's without looking very deeply into the probem.

However, this does suggest that there is a simple text-processing, 
search-and-replace workaround if you are able/prepared to post-process 
the SVG (or you could post-process it "properly" with the 'XML' package).

Paul

> Jeroen
>
> --
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>
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-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/