tim@jemimah:~$ isatool mkdir HOL MySession 
Preparing session "MySession" ...          
creating ./IsaMakefile                     
creating ./MySession/ROOT.ML               
creating ./MySession/document              
creating ./MySession/document/root.tex     

Notes:

  * 'isatool make' processes the session (including document preparation)

  * ./IsaMakefile contains compilation options and file dependencies

  * ./MySession/document/root.tex contains the LaTeX master document setup

  * ./MySession/ROOT.ML needs to contain ML code to load all theories

tim@jemimah:~$ isatool make
Running HOL-MySession ...  
Browser info at /home/tim/isabelle/browser_info/HOL/MySession
HOL-MySession FAILED                                         
(see also /home/tim/isabelle/heaps/Isabelle2008/polyml-5.2_x86-linux/log/HOL-MySession)

Enter file name: 
! Emergency stop.
<read *>         
                 
l.198 \let       
          \fmtname\isafmtname^^M
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on root.log.                          
Document preparation failure in directory '/home/tim/isabelle/browser_info/HOL/MySession/document'
*** No document: "/home/tim/isabelle/browser_info/HOL/MySession/document.pdf"                     

make: *** [/home/tim/isabelle/heaps/Isabelle2008/polyml-5.2_x86-linux/log/HOL-MySession.gz] Error 1
tim@jemimah:~$ pdflatex -version
pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
kpathsea version 3.5.6                                   
Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX using libpoppler copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX using libpoppler source.
Primary author of pdfTeX using libpoppler: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Kpathsea written by Karl Berry, Olaf Weber, and others.

Compiled with libpng 1.2.27; using libpng 1.2.27
Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
Compiled with libpoppler version 3.00