I have figured it out. It turns out that it is not a R problem. libfontconfig.so.1 links to libfreetype, it happens that there are two sets of libfreetype files in my system, one from Ubuntu and another from xampp. When the php script is run to invoke R it uses the libfreetype files in /opt/lampp/lib which are out of date, so R/cairo.so could not load. Copying the updated version of libfreetype* from /usr/lib/i386-linux-gnu/ into /opt/lampp/lib overwritting the outdated version solved the problem. I suppose I could also change some environmental variables with something like export LD_LIBRARY_PATH= /usr/lib/i386-linux-gnu/
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