This is all a bit advanced for me. All I can do about encoding is change the 
way I export to bibtex from zotero and I choose utf8 for that, but I don't know 
were else I can change encoding in my lyx file.

I created a new lyx file, a new library in zotero, exported it in the same 
folder as y file, tried ti add citation and the same thing happens.

I then tried the terminal, although I don't know what it does actually... I got 
this (if this is understandable by any of you I would really appreciate some 
help):

_________________________________________________
(Press Enter to retry, or Control-D to exit)
Please type another input file name: 
/Users/weremoose/thesis/managing_nuclear_factories.lyx
(/Users/weremoose/thesis/managing_nuclear_factories.lyx
LaTeX2e <2005/12/01>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, german-x-2008-06-18, ngerman-x-2008-06-18, ancientgreek, ibycus, ar
abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc
h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono
greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, la
tin, lithuanian, mongolian, mongolian2a, bokmal, nynorsk, polish, portuguese, r
omanian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turki
sh, ukenglish, ukrainian, uppersorbian, welsh, loaded.
! You can't use `macro parameter character #' in vertical mode.
l.1 #
     LyX 1.6.5 created this file. For more info see http://www.lyx.org/
? bibtex /Users/weremoose/thesis/thesis_library.bib
Type <return> to proceed, S to scroll future error messages,
R to run without stopping, Q to run quietly,
I to insert something, E to edit your file,
1 or ... or 9 to ignore the next 1 to 9 tokens of input,
H for help, X to quit.
? 

! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.1 #L
      yX 1.6.5 created this file. For more info see http://www.lyx.org/
? 
! Undefined control sequence.
l.2 \lyxformat
               345
? latex /Users/weremoose/thesis/managing_nuclear_factories.lyx
Type <return> to proceed, S to scroll future error messages,
R to run without stopping, Q to run quietly,
I to insert something, E to edit your file,
1 or ... or 9 to ignore the next 1 to 9 tokens of input,
H for help, X to quit.
? /Users/weremoose/thesis/managing_nuclear_factories.lyx
Type <return> to proceed, S to scroll future error messages,
R to run without stopping, Q to run quietly,
I to insert something, E to edit your file,
1 or ... or 9 to ignore the next 1 to 9 tokens of input,
H for help, X to quit.
? /Users/weremoose/thesis/managing_nuclear_factories.lyx
Type <return> to proceed, S to scroll future error messages,
R to run without stopping, Q to run quietly,
I to insert something, E to edit your file,
1 or ... or 9 to ignore the next 1 to 9 tokens of input,
H for help, X to quit.
? 
! Undefined control sequence.
l.5 \textclass
               scrbook
? 
! Undefined control sequence.
l.6 \use
        _default_options true
? 
! Missing $ inserted.
<inserted text> 
                $
l.6 \use_
         default_options true
? 
_________________________________________________

Any ideas? I am lost here, I am actually thinking of putting the citations 
manually in my document as footnotes... I don't know what to do...

Thanks again...


On Jan 7, 2010, at 8:42 PM, Pierfranco Minsenti wrote:

> Hello,
> 
> in my experience I have obtained the question marks ? in the PDF file 
> obtained from LyX, instead of regular citations, in these 2 cases:
> 1) as Richard said: when LyX doesn't find the bibtex file, maybe because it 
> has been moved after inserting citations
> AND / OR
> 2) when there is something wrong with the bibliographic style selected.
> 
> Since weremoose says he was able to insert citations using the LyX commands, 
> the file path should be right (at least at the moment of inserting 
> citations). So one reason for the problem could be the second one. I would 
> suggest to try to select different bibliographic styles from the proper menu 
> and then save the file and compile in order to verify if this could be the 
> problem.
> 
> pierfranco
> 
> 
> 2010/1/7 rgheck <[email protected]>
> On 01/07/2010 09:23 AM, weremoose wrote:
> Hello,
> 
> I am a mac user (currently on 10.6.2) and I decided to use LyX to write my
> thesis as it looked very promising. So I have LyX 1.6.5 installed and
> started testing it, it's very convenient and gets me nice looking text even
> with my drafts. Everything good so far. I found that I can use Zotero for my
> references, installed it along with lyz, everything works fine now and my
> citations are pushed to LyX.
> 
> The thing is, there must be some kind of bug and no matter how much I tried
> I can't get it to work. I've been trying for more than a week and I feel
> quite stupid... I am inserting my BibTex generated bibliography at the end
> of my document, I select my database file, I add citations, fine, but the
> citations just don't want to show up in my pdf file. I tried changing the
> document style, nothing (I am using book-komma-script) I tried the
> bibliography preferences with all the citation options, I tried latex
> export, I tried dvi preview, I tried pdf preview, all I get is instead of my
> references a questionmark [?] or ? depending on the citation preferences and
> no bibliography in the end. I tried to use different citation styles as
> well, it is still not working.
> 
>   
> One common reason for this is that the BibTeX file has the wrong sort of 
> encoding, in particular, that you are somewhere using Unicode characters that 
> are confusing the BibTeX processor. This is especially likely if you have 
> tried exporting to LaTeX and running everything manually. Indeed, that is the 
> best way to debug this kind of problem: Export to LaTeX; run the LaTeX 
> sequence manually from a terminal ("latex myfile"; then "bibtex myfile"; then 
> "latex myfile"; then "latex myfile" again, if necessary) and watch for error 
> messages. You will see undefined citations the first latex run; this is 
> normal and is why you need to run bibtex. It's on the bibtex run that you'll 
> see what's causing the problem. As I said, quite possibly encoding issues.
> 
> If things DO work properly when you run things manually, then the problem is 
> elsewhere. It could be that LyX isn't finding your bibliography file; it 
> could be that lyz (which is very know) is doing something wrong.
> 
> Richard
> 
> 
> 
> 

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