Oh, that is far in the opposite direction now -- too much debug
information :) You do not need to turn on debug messages; normal
messages are enough.

The problem comes from:

  Rscript --verbose --no-save --no-restore "/Applications/LyX


--slave --no-restore --no-save --no-restore --file=/Applications/LyX

I do not know why R removed the quotes around the --file argument, but
FWIW, can you upgrade R to the latest version before you proceed? Also
update LyX if you can. Both LyX and R are old in your system.

The other thing is to make sure you did not hack at the Sweave module
by yourself; check the preferences file in your LyX User directory
(should not contain anything about Sweave there).

I do not use Mac OS, so it is difficult for me to reproduce the problem.

Yihui Xie <xieyi...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

On Thu, Jul 26, 2012 at 10:40 AM, Hobbs,Tom <tom.ho...@colostate.edu> wrote:
> Sorry--I thought the message I sent was the one you needed.  I set all of
> the debug messages to Yes and it appears that this is the one causing
> problems:
> 08:34:14.849: Fatal error: cannot open file '/Applications/LyX': No such
> file or directory
> There is a file in my /Applications directory for LyX 2.app
> I included the full message list below.
> I have done the Reconfigure and the problem remains.
> Thanks very much for your help.
> Tom

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