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I update today to TeX Live 2013 (MacTeX) from TeX Live 2012. On my .tex document (that was perfectly working until yesterday) I run and get in the mini-buffer:

1) latex -> You should run Biber to get citation right (This is new, yesterday it asked me for BibLaTeX...)

2) biber -> Biber finished successfully. Run LaTex again to get citations right

3) latex -> LaTeX: There were unresolved citations

I did update with TeX Live Utility all the packages, I restarted my Mac. Still same problem.

\documentclass[a4paper]{article}

% Set the values for the biblography
\usepackage[
    backend=biber,
    isbn=false,
    url=false,
    doi=false,
    eprint=false,
]{biblatex}

%Point to the bibliography db
\addbibresource{mybib.bib}

\begin{document}

\fullcite{egghead2013} 

\textcite[][361]{egghead2013} %three times, on more pages...

\end{document}

This is my output after the last step:

Running `LaTeX' on `document' with ``pdflatex --synctex=1 -interaction=nonstopmode "\input" document.tex''
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(./document.tex
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/size10.clo))
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/biblatex.sty 
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/biblatex2.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/etoolbox/etoolbox.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/etex-pkg/etex.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))
(/usr/local/texlive/2013/texmf-dist/tex/latex/logreq/logreq.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/logreq/logreq.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/blx-dm.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/blx-compat.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/biblatex.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/bbx/numeric.bbx
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/bbx/standard.bbx))
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/cbx/numeric.cbx)
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgfplots/pgfplotstable.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplots.revision.tex)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgfplots/pgfplots.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplots.revision.tex)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/frontendlayer/tikz.sty
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(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfutil-common.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfutil-latex.def
(/usr/local/texlive/2013/texmf-dist/tex/latex/ms/everyshi.sty))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfrcs.code.tex))
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(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/systemlayer/pgf.cfg)
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(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/systemlayer/pgfsyssoftpath.
code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/systemlayer/pgfsysprotocol.
code.tex)) (/usr/local/texlive/2013/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcore.code.tex
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tex
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code.tex)
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(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/math/pgfmathfunctions.misc.
code.tex)))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/math/pgfmathfloat.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex)
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(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcoreexternal.
code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/basiclayer/pgfcorepatterns.
code.tex)))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/modules/pgfmoduleshapes.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/modules/pgfmoduleplot.code.
tex)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/utilities/pgffor.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/utilities/pgfkeys.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgffor.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/modules/pgfmodulematrix.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopaths.code.tex)))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplots.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplotscore.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/sys/pgfplotssysgeneric.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/libs/pgfplotslibrary.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_loader.code.tex
Package pgfplots: loading complementary code for your PGF version...

(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_misc.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgfkeys.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgfkeysfiltered.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgfmathfloat.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgflibraryplothandlers.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgflibraryfpu.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgfcorescopes.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/oldpgfcompatib/pgfplotsoldpgfsupp_pgfcorelayers.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/util/pgfplotsutil.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/liststructure/pgfplotsliststructure.code.tex)
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(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/numtable/pgfplotstableshared.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/liststructure/pgfplotsdeque.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/util/pgfplotsbinary.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/util/pgfplotsbinary.data.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/util/pgfplotsutil.verb.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/libs/pgflibrarypgfplots.surfshading.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/sys/pgflibrarypgfplots.surfshading.pgfsys-pdftex.def)))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/util/pgfplotscolormap.
code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/util/pgfplotscolor.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplotsstackedplots.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplotsplothandlers.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplotsmeshplothandler.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplots.scaling.code.
tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplotscoordprocessing.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplotsticks.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplots.paths.code.tex)
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarydecorations.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/modules/pgfmoduledecorations.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarydecorations.pathmorphing.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/libraries/decorations/pgflibrarydecorations.pathmorphing.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarydecorations.pathreplacing.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/libraries/decorations/pgflibrarydecorations.pathreplacing.code.tex)))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryplotmarks.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/libraries/pgflibraryplotmarks.code.tex)))
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/numtable/pgfplotstable.code.tex
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/numtable/pgfplotstable.coltype.code.tex))
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/array.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/caption/caption.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/caption/caption3.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
(./document.aux (./bib/egghead2013.aux))
(./document.bbl) ABD: EveryShipout initializing macros
(/usr/local/texlive/2013/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ifpdf.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
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Package pgfplots Warning: running in backwards compatibility mode (unsuitable tick labels; missing features). Consider writing \pgfplotsset{compat=1.8} into your preamble.
 on input line 38.

[1{/usr/local/texlive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(./bib/egghead2013.tex

LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 1.


LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 16.


LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 16.


Overfull \hbox (2.80838pt too wide) in paragraph at lines 30--32
 [][] 

LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 32.


LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 32.


Overfull \hbox (14.48819pt too wide) in paragraph at lines 45--47
 [][] 

LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 47.


LaTeX Warning: Citation 'egghead2013' on page 2 undefined on input line 47.

) [2] [3] (./document.aux (./bib/egghead2013.aux))

LaTeX Warning: There were undefined references.


Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)                document
(biblatex)                and rerun LaTeX afterwards.

 )
(see the transcript file for additional information)</usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx8.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on document.pdf (3 pages, 112516 bytes).
SyncTeX written on document.synctex.gz.
Transcript written on document.log.

LaTeX finished at Wed Aug 14 09:07:38

And finally my output after biber:

Running `Biber' on `document' with ``biber document''
INFO - This is Biber 1.7
INFO - Logfile is 'document.blg'
INFO - Reading 'document.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'mybib.bib' for section 0
INFO - Found BibTeX data source 'mybib.bib'

Biber abort trap: 6 at Wed Aug 14 09:33:22

And running biber --debug document.bcf from shell I get the same

INFO - This is Biber 1.7
INFO - Logfile is 'document.blg'
INFO - DEBUG mode: all messages are logged to 'document.blg'
INFO - Reading 'document.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'mybib.bib' for section 0
INFO - Found BibTeX data source 'mybib.bib'
zsh: abort      biber --debug document.bcf
share|improve this question
    
biber is completing successfully and the output ends with the line: Biber abort trap: 6 at Wed Aug 14 09:33:22? –  jon Aug 14 '13 at 1:14
    
Exactly. "Biber finished successfully. Run LaTex again to get citations right" is what I get in the little-buffer after running biber. And that other is the "Output Buffer". –  Francesco Aug 14 '13 at 1:42
    
Yes, sorry I meant mini-buffer (for little-buffer). I edited the question adding the result from running --debug from command line. I doesn't add anything. –  Francesco Aug 14 '13 at 4:23
1  
Then I think biber is aborting too soon. Actually, your last INFO message is only about halfway through the normal output. Normally, it should end with lines like: INFO - Writing '<file>.bbl' with encoding 'UTF-8' and INFO - Output to <file>.bbl. (I'm deleting my earlier comments, since they are unlikely to be helpful in the future.) –  jon Aug 14 '13 at 5:16
1  
We need a full MWE with your .bib to see what's happening. –  PLK Aug 14 '13 at 5:33

1 Answer 1

I kind of fix the problem simply by replacing backend=biber with backend=bibtex and then run "Bibtex" instead of "Biber". I got the pdf output then with all the references right.

share|improve this answer

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