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read.table( ... comment.char="#") truncated my data

The default has been "#" since version 1.4.0, that is for the last *five*
releases of R.  Changing *now* would be `not compatible earlier versions
of R'.
On Fri, 11 Oct 2002 Ren_Yu at hgsi.com wrote:

            
Yes, and it is easy for you to do: see read.csv for a hint about how to do
so.