Just a couple of small bug-lets/stuffs in Sweave: - It stripes off the two lines starting with @ (this is a verbatim section showing plink's start-up message): ====================================== @----------------------------------------------------------@ | PLINK! | v0.99p | 17/Dec/2006 | |----------------------------------------------------------| | (C) 2006 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@ ======================================= - XeTeX definitely does not like having any \usepackage[whatever]{inputenc} (it assumes inputs are always utf-8) While both of these can be worked around - using \input{} for anything Sweave might mess with, and put a % in front of \userpackage[inputenc] (Sweave seems to read LaTeX comments as real; but that's probaby a mis-feature...); SWeave probably should not stripe @ without a starting <<>>= noweb marker. Had a couple of discussion elsewhere - it seems that international stuff in LaTeX, XeTeX and/or LuaTeX are the main ones to use, but for most parts people still stick to regional encodings (e.g. iso 8859-11 for Thai) so dependences on inputenc is not really useful. FWIW.