Bibliography problem and [?] questionmarks

[weremoose]

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.

I am not an advanced user (that is why I chose LyX) but it is very
frustrating and I can't seem to get it starting, I know that once I have it
running I will be thankful but I am not there yet...

Anyone having same kind of problem? Have you heard of this before? Any
suggestions?:confused:

Thanks a lot...

[rgheck]

Post by weremoose
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

[Pierfranco Minsenti]

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

Post by rgheck

Post by weremoose
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

[Anastasia Melekou]

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...

Post by weremoose
Hello,
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
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

[stephen's mailinglist account]

Post by Anastasia Melekou
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.

Occasionally I have had similar problems with missing bibliography
items - almost always the problem seems to be from BibTeX entries that
I have copied the titles directly from pdfs and the offending
characters seem to generally be right or left quotes or em-dashes that
bibTeX cannot cope with. I suspect that characters with Unlauts etc
may also cause problems.
When I clean up the offending entries - everything works