"Why did read.table stop reading my file" is a pretty FAQ, e.g.
http://thread.gmane.org/gmane.comp.lang.r.general/297406/focus=297409
(I could come up with a lot more examples if someone wanted).
The answer is typically "check for spurious comment characters and
unmatched quotation marks"
Does this seem FAQ-worthy? Should I e-mail the FAQ maintainer and suggest
it?
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