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So, I just installed the latest TeX Live manually from the website on an Ubuntu 11.10 64bit. I left every path on the default one, I installed all the packages. Then I installed the latest version of Texmaker.

I just had to manually fix in the option all the command, to make them point to the

/usr/local/texlive/2012/bin/x86_64-linux/'command'

So far everything nice and good, F2 LaTeX is working as supposed to do; no problems; PDF preview fine as well. Problem arises when I tried to add bibliography:

\bibliographystyle{plain}
\bibliography{/home/elect/Dropbox/Poli/toptesi/Ref}

It doesn't work. I get problems. I don't know which ones, because it is not shown.

Then I tried to run the command manually:

elect@elect-desktop:/usr/local/texlive/2012/bin$ bibtex /home/elect/Dropbox/Poli/toptesi/References
I couldn't open file name `/home/elect/Dropbox/Poli/toptesi/References.aux'

Why is it looking for .aux file?

Edit: as Guido suggested, I ran on the tex file:

elect@elect-desktop:~$ bibtex /home/elect/Dropbox/Poli/toptesi/toptesi-example.aux 

bibtex: Not writing to /home/elect/Dropbox/Poli/toptesi/toptesi-example.blg (openout_any = p).
I couldn't open file name `/home/elect/Dropbox/Poli/toptesi/toptesi-example.blg'

Edit2:

elect@elect-desktop:~/Dropbox/Poli/toptes$ pdflatex toptesi-example
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 restricted \write18 enabled.
entering extended mode
(./toptesi-example.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, uk
english, usenglishmax, italian, loaded.
(./toptesi.cls
Document Class: toptesi 2012/10/06 v.5.61b Class for typesetting university the
ses
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/report.cls
Document Class: report 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/size12.clo))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/babel/babel.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/babel/english.ldf
(/usr/local/texlive/2012/texmf-dist/tex/generic/babel/babel.def))
(/usr/local/texlive/2012/texmf-dist/tex/generic/babel/italian.ldf)))
(./toptesi.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(./topfront.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/etoolbox/etoolbox.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/etex-pkg/etex.sty))
(./toptesi.cfg)) (./topcoman.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))))
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/latin1.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/lmodern.sty)
(./toptesi-example.aux)
(/usr/local/texlive/2012/texmf-dist/tex/generic/babel/lgrcmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/t1lmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
Messaggio Toptesi: Ricalcolo i margini
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./toptesi-example.out) (./toptesi-example.out)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/ot1lmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omllmm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omslmsy.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omxlmex.fd)
Overfull \vbox (2.16994pt too high) has occurred while \output is active
[1{/usr/local/texlive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
[2] (./toptesi-example.toc)
! I can't write on file `toptesi-example.toc'.
<to be read again> 
                   \relax 
\@starttoc ... tf@#1\endcsname \jobname .#1\relax 
                                                  \fi \@nobreakfalse \endgroup 

\tableofcontents ...contentsname }\@starttoc {toc}
                                                  \clearpage \if@restonecol ...

\indici ... \frontmattertrue \fi \tableofcontents 
                                                  \iftablespage {\addvspace ...
l.127 \indici

(Press Enter to retry, or Control-D to exit; default file extension is `.tex')
Please type another output file name: 

Edit3:

Now on >pdflatex I get:

! LaTeX Error: Something's wrong--perhaps a missing \item. 

My bib entry is the follow:

\bibliographystyle{plain} \bibliography{References} 
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closed as too localized by lockstep, Andrew Swann, Stefan Kottwitz Nov 20 '12 at 11:35

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You have to run bibtex on the filename of the latex file (without file extension). –  Guido Oct 28 '12 at 0:50
    
@Guido It still doesnt work.. –  elect Oct 28 '12 at 8:48
    
try from the terminal (command line), go to the working directory, cd /home/elect/Dropbox/Poli/toptesi and then run pdflatex toptesi-example and then run bibtex toptesi-example –  Guido Oct 28 '12 at 9:12
    
@Guido weird, toptesi-example.toc is there, inside my home, I am the owner, read/write rights... –  elect Oct 28 '12 at 9:18
    
you can try by removing all auxiliary files. –  Guido Oct 28 '12 at 9:22

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