mheil@biolaptop:~/doxygen_problem$ doxygen --version
1.7.4
mheil@biolaptop:~/doxygen_problem$ doxygen -g


Configuration file `Doxyfile' created.

Now edit the configuration file and enter

  doxygen Doxyfile

to generate the documentation for your project

mheil@biolaptop:~/doxygen_problem$ doxygen 
Searching for include files...
Searching for example files...
Searching for images...
Searching for dot files...
Searching for msc files...
Searching for files to exclude
Searching for files to process...
Searching for files in directory /home/mheil/doxygen_problem
Reading and parsing tag files
Preprocessing /home/mheil/doxygen_problem/doxygen_problem.h...
Parsing file /home/mheil/doxygen_problem/doxygen_problem.h...
Building group list...
Building directory list...
Building namespace list...
Building file list...
Building class list...
Associating documentation with classes...
Computing nesting relations for classes...
Building example list...
Searching for enumerations...
Searching for documented typedefs...
Searching for members imported via using declarations...
Searching for included using directives...
Searching for documented variables...
Building member list...
Searching for friends...
Searching for documented defines...
Computing class inheritance relations...
Computing class usage relations...
Flushing cached template relations that have become invalid...
Creating members for template instances...
Computing class relations...
Add enum values to enums...
Searching for member function documentation...
Building page list...
Search for main page...
Computing page relations...
Determining the scope of groups...
Sorting lists...
Freeing entry tree
Determining which enums are documented
Computing member relations...
Building full member lists recursively...
Adding members to member groups.
Computing member references...
Inheriting documentation...
Generating disk names...
Adding source references...
Adding xrefitems...
Sorting member lists...
Counting data structures...
Resolving user defined references...
Finding anchors and sections in the documentation...
Combining using relations...
Adding members to index pages...
Generating style sheet...
Generating search indices...
Generating index page...
Generating page index...
Generating example documentation...
Generating file sources...
Generating code for file doxygen_problem.h...
Generating file documentation...
Generating page documentation...
Generating group documentation...
Generating group index...
Generating class documentation...
Generating annotated compound index...
Generating alphabetical compound index...
Generating hierarchical class index...
Generating member index...
Generating namespace index...
Generating namespace member index...
Generating graph info page...
Generating file index...
Generating example index...
Generating file member index...
finalizing index lists...
finished...
mheil@biolaptop:~/doxygen_problem$ cd latex/
mheil@biolaptop:~/doxygen_problem/latex$ make
rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out refman.pdf
pdflatex refman.tex
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
entering extended mode
(./refman.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty)
(/etc/texmf/tex/latex/config/graphics.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)))
(/usr/share/texmf-texlive/tex/latex/tools/multicol.sty)
(/usr/share/texmf-texlive/tex/latex/float/float.sty)
(/usr/share/texmf-texlive/tex/latex/listings/listings.sty
(/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty)
(/usr/share/texmf-texlive/tex/latex/listings/listings.cfg))
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg))
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf/tex/latex/xcolor/xcolor.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/colortbl/colortbl.sty
(/usr/share/texmf-texlive/tex/latex/tools/array.sty)))
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/home/mheil/tex/STYLES/hyperref.sty (/home/mheil/tex/STYLES/pd1enc.def)
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/home/mheil/tex/STYLES/puenc.def)
Implicit mode ON; LaTeX internals redefined
(/home/mheil/tex/STYLES/backref.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty))
*hyperref using driver hpdftex*
(/home/mheil/tex/STYLES/hpdftex.def
(/usr/share/texmf-texlive/tex/latex/psnfss/pifont.sty
(/usr/share/texmf-texlive/tex/latex/psnfss/upzd.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/upsy.fd)))
(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)))
(/usr/share/texmf-texlive/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/courier.sty)
(/usr/share/texmf-texlive/tex/latex/sectsty/sectsty.sty)
(/usr/share/texmf-texlive/tex/latex/tocloft/tocloft.sty

Package tocloft Note: The document has chapter divisions.

) (./doxygen.sty (/usr/share/texmf-texlive/tex/latex/tools/calc.sty)
(/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def)))
(/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty)
(/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty)
(/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty)
Writing index file refman.idx
No file refman.aux.
(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd)
(/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/home/mheil/tex/STYLES/nameref.sty) [1{/var/lib/texmf/fonts/map/pdftex/updma
p/pdftex.map}] [2] (/usr/share/texmf-texlive/tex/latex/psnfss/ot1phv.fd)
[1] [2]
Chapter 1.
(./index.tex (/usr/share/texmf-texlive/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omxztmcm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1ptm.fd))
No file refman.ind.
[1] (./refman.aux)

LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 ){/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texli
ve/fonts/type1/urw/helvetic/uhvb8ac.pfb></usr/share/texmf-texlive/fonts/type1/u
rw/helvetic/uhvr8a.pfb>
Output written on refman.pdf (5 pages, 18499 bytes).
Transcript written on refman.log.
makeindex refman.idx
This is makeindex, version 2.15 [TeX Live 2009] (kpathsea + Thai support).
Scanning input file refman.idx...done (0 entries accepted, 0 rejected).
Nothing written in refman.ind.
Transcript written in refman.ilg.
pdflatex refman.tex
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
entering extended mode
(./refman.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty)
(/etc/texmf/tex/latex/config/graphics.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)))
(/usr/share/texmf-texlive/tex/latex/tools/multicol.sty)
(/usr/share/texmf-texlive/tex/latex/float/float.sty)
(/usr/share/texmf-texlive/tex/latex/listings/listings.sty
(/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty)
(/usr/share/texmf-texlive/tex/latex/listings/listings.cfg))
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg))
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf/tex/latex/xcolor/xcolor.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/colortbl/colortbl.sty
(/usr/share/texmf-texlive/tex/latex/tools/array.sty)))
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/home/mheil/tex/STYLES/hyperref.sty (/home/mheil/tex/STYLES/pd1enc.def)
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/home/mheil/tex/STYLES/puenc.def)
Implicit mode ON; LaTeX internals redefined
(/home/mheil/tex/STYLES/backref.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty))
*hyperref using driver hpdftex*
(/home/mheil/tex/STYLES/hpdftex.def
(/usr/share/texmf-texlive/tex/latex/psnfss/pifont.sty
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(/usr/share/texmf-texlive/tex/latex/psnfss/upsy.fd)))
(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
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(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)))
(/usr/share/texmf-texlive/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/courier.sty)
(/usr/share/texmf-texlive/tex/latex/sectsty/sectsty.sty)
(/usr/share/texmf-texlive/tex/latex/tocloft/tocloft.sty

Package tocloft Note: The document has chapter divisions.

) (./doxygen.sty (/usr/share/texmf-texlive/tex/latex/tools/calc.sty)
(/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def)))
(/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty)
(/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty)
(/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty)
Writing index file refman.idx
(./refman.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd)
(/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/home/mheil/tex/STYLES/nameref.sty) (./refman.out) (./refman.out) [1{/var/li
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(/usr/share/texmf-texlive/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omxztmcm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1ptm.fd)) [1] [2]
Chapter 1.
(./index.tex) (./refman.ind) [1] (./refman.aux) ){/usr/share/texmf-texlive/font
s/enc/dvips/base/8r.enc}</usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvb
8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvb8ac.pfb></usr/sha
re/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb>
Output written on refman.pdf (5 pages, 24153 bytes).
Transcript written on refman.log.
latex_count=5 ; \
	while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $latex_count -gt 0 ] ;\
	    do \
	      echo "Rerunning latex...." ;\
	      pdflatex refman.tex ;\
	      latex_count=`expr $latex_count - 1` ;\
	    done
