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With the option tidy=T, each Sinput environment gets a spurious blank line. This can be seen with the following example file:
\documentclass{article}
\begin{document}
\SweaveOpts{highlight=FALSE}
\begin{Scode}{print=TRUE,cache=TRUE,tidy=TRUE}
1+1
\end{Scode}
\end{document}
which gives this output after R CMD pgfsweave test.Rtex (excerpted from the long .tex file generated):
\begin{Schunk}
\begin{Sinput}
> 1 + 1
\end{Sinput}
\end{Schunk}
The blank line should not be present, and leads to extra blank space in the pdf document. I think this is due to line 484 in R/pgfSweaveDriver.R, where a blank line is emitted if options$highlight or $tidy is true.
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