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prefixed.lines Parser Function (in inlinedocs/R/parsers.R), and
furthermore I could tell this was occuring when is.arg() was being
called within prefixed.lines. In fact the problem was related to an
algorithm that matches open and close parentheses to detemine the
start of the body of the function.

Sorry that the piece of your code that was causing the error wasn't
more clearly indicated. I don't really know how I would implement
something like this in inlinedocs, since it doesn't necessarily parse
the input line-by-line.

Anyways, the bugfix is just checked into inlinedocs SVN on R-Forge, so
you can check out the new version and get back to work with

svn checkout svn://svn.r-forge.r-project.org/svnroot/inlinedocs