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The arguments in texidvi() are rarely used, but those in Sweave() are often very important. In #25 I mentioned changes in the official Sweave, and now I noticed the file encoding might cause problems.
Sweave() was changed so that it will no longer respect options('encoding'); instead, it takes the encoding information from either \usepackage[foo]{inputenc} or Sweave(..., encoding = 'foo'). Since pgfSweave() passes ... to texi2dvi(), it seems to be impossible to pass the encoding directly via command line, so the only way is to use \usepackage[foo]{inputenc}.
I'm not completely sure if this can bring a real problem, but I believe it is more useful to pass ... to Sweave() and more consistent with the usage of Sweave().
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