Okay, I've almost cleaned up all warnings, 2 more remain...
The full log can be found here: http://paste.pocoo.org/show/158051/
However, the important bits are as follows...
Problem 1...
....
Package hyperref Warning: Wrong driver `hdvipson.def';
(hyperref) pdfTeX is running in PDF mode.
(hyperref) Forcing driver `hpdftex.def'.
*hyperref using driver hpdftex*
(/usr/local/texlive/2009/texmf-dist/tex/latex/hyperref/hpdftex.def)
(/usr/local/texlive/2009/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
....
Problem 2...
...
LaTeX Font Warning: Size substitutions with differences
(Font) up to 4.0pt have occurred.
) </Users/nima/.texlive2009/texmf-var/fonts/pk/ljfour/public/mathabx/
mathx10.7
20pk> </Users/nima/.texlive2009/texmf-var/fonts/pk/ljfour/public/
mathabx/matha8
.600pk> </Users/nima/.texlive2009/texmf-var/fonts/pk/ljfour/public/
mathabx/m...
...
Any ideas?
Nima
it would appear that you have the "dvipsone" option in your call to
hyperref, but aren't using the y&y system. in most cases, you don't
need a driver option at all (hyperref can make up its own mind); in
this case, hyperref is reporting that your driver option is
inconsistent with using pdflatex.
>Problem 2...
>...
>
>LaTeX Font Warning: Size substitutions with differences
>(Font) up to 4.0pt have occurred.
for at least one of your fonts, latex believes you only have a fixed
range of sizes available; at some stage, you've asked for a size of
that font that's 4.0pt away from the nearest size available.
there ought to be a warning somewhere in the log saying something like:
LaTeX Font Warning: Font shape `OT1/cmr/m/n' in size <30> not available
(Font) size <24.88> substituted on input line 0.
in your case, there will be a useful line number (i got that error by
typing at latex from the console), and the font shape will given you
further details.
i can't actually find any such warning in your posted log, so i'm at
the limit of what i can do to help.
--
Robin Fairbairns, Cambridge
That resolved the wrong-driver issue - I removed the line...
dvipsone=pdftex, % or dvips
...all together and let it figure it for itself.
I'll dig around with the other one and see if I can figure out which
font it's referring to.
Thanks again :)
Nima