references not printing

Question

I've googled this (seems to be a problem others are having) and tried numerous things to no avail (including reinstalling both JabRef and MikTEx). 3 hours later I'm broken. My woes started when I deleted MikTex from my system and then reinstalled (I thought I was updating turns out 2.9 was what I had already). Now when I run mikTex no references in my documents will print (The PDF outputs with no reference section and the in text citations are bolded as if they don't exist or JabRef and MikTex aren't communicating).

Thank you in advance.

Here's what I'm using:

\documentclass[leavefloats]{apa6e}
\usepackage[american]{babel}
\usepackage{csquotes}
\usepackage[style=apa]{biblatex}
\addbibresource{Psychometrics}
\DeclareLanguageMapping{american}{american-apa}
\usepackage{enumerate}
\usepackage{hyperref}
\usepackage{graphicx}
\usepackage{ragged2e}
\usepackage{textcomp}
\usepackage[section]{placeins}
\usepackage{setspace}
\usepackage{appendix}
\usepackage{float}
\usepackage{subfig}
\usepackage{amsmath}
\usepackage{color}
\usepackage{ifthen}
\defbibheading{bibliography}{%
\section{\normalfont\refname}}
\title{TITLE}
\shorttitle{TITLE}
\author{ME}
\authornote{Nothing}
\date{\today}
\begin{document}
\maketitle

stuff

\cite{Bennett1954}
\clearpage 
\printbibliography
\end{document}

I'm using MikTex 2.9 with JabRef 2.8 with winEdt 7 on a win 7 machine. The bib file Psychometrics.bib is located in the directory that the .tex file is located.

Here's the output:

Command Line:   bibtex.exe "example"
Startup Folder: C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final paper

This is BibTeX, Version 0.99d (MiKTeX 2.9)
The top-level auxiliary file: example.aux
I found no \citation commands---while reading file example.aux
I found no \bibdata command---while reading file example.aux
I found no \bibstyle command---while reading file example.aux
(There were 3 error messages)


Command Line:   texify.exe --pdf --tex-option=--interaction=errorstopmode --tex-option=--synctex=-1 "C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final paper\example.tex"
Startup Folder: C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final paper

This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9)
entering extended mode

("C:/Users/trinker/Desktop/PhD Program/CEP 510 Psychometrics/Assignments/Final 
paper/example.tex"
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, afrikaans, ancientgreek, ar
abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan, coptic, 
croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish, french, ga
lician, german, german-x-2009-06-19, greek, gujarati, hindi, hungarian, iceland
ic, indonesian, interlingua, irish, italian, kannada, kurmanji, lao, latin, lat
vian, lithuanian, malayalam, marathi, mongolian, mongolianlmc, monogreek, ngerm
an, ngerman-x-2009-06-19, nynorsk, oriya, panjabi, pinyin, polish, portuguese, 
romanian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, swis
sgerman, tamil, telugu, turkish, turkmen, ukenglish, ukrainian, uppersorbian, u
senglishmax, welsh, loaded.
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\apa6e\apa6e.cls
Document Class: apa6e 2011/03/03 v0.3 APA 6e manuscript formatting
("C:\MiKTeX 2.9\tex\latex\base\article.cls"
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
("C:\MiKTeX 2.9\tex\latex\base\size12.clo"))
("C:\MiKTeX 2.9\tex\latex\psnfss\times.sty")
("C:\MiKTeX 2.9\tex\latex\psnfss\mathptmx.sty")
("C:\MiKTeX 2.9\tex\latex\geometry\geometry.sty"
("C:\MiKTeX 2.9\tex\latex\graphics\keyval.sty")
("C:\MiKTeX 2.9\tex\generic\oberdiek\ifpdf.sty")
("C:\MiKTeX 2.9\tex\generic\oberdiek\ifvtex.sty")
("C:\MiKTeX 2.9\tex\generic\ifxetex\ifxetex.sty")
("C:\MiKTeX 2.9\tex\latex\geometry\geometry.cfg"))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\ms\ragged2e.sty
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\ms\everysel.sty)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\footmisc\footmisc.sty))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\fancyhdr\fancyhdr.sty)
("C:\MiKTeX 2.9\tex\latex\float\float.sty")
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\caption\caption.sty
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\caption\caption3.sty))
("C:\MiKTeX 2.9\tex\latex\base\ifthen.sty"))
("C:\MiKTeX 2.9\tex\generic\babel\babel.sty"
*************************************
* Local config file bblopts.cfg used
*
("C:\MiKTeX 2.9\tex\latex\00miktex\bblopts.cfg")
("C:\MiKTeX 2.9\tex\generic\babel\english.ldf"
("C:\MiKTeX 2.9\tex\generic\babel\babel.def")))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\csquotes\csquotes.sty
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\etoolbox\etoolbox.sty
("C:\MiKTeX 2.9\tex\latex\misc\etex.sty"))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\csquotes\csquotes.def)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\csquotes\csquotes.cfg))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\biblatex.sty

Package biblatex Warning: No "backend" specified, using Biber backend.
(biblatex)                To use BibTeX, load biblatex with 
(biblatex)                the "backend=bibtex" option.

(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\biblatex2.sty
("C:\MiKTeX 2.9\tex\latex\oberdiek\kvoptions.sty"
("C:\MiKTeX 2.9\tex\generic\oberdiek\ltxcmds.sty")
("C:\MiKTeX 2.9\tex\generic\oberdiek\kvsetkeys.sty"
("C:\MiKTeX 2.9\tex\generic\oberdiek\infwarerr.sty")
("C:\MiKTeX 2.9\tex\generic\oberdiek\etexcmds.sty"
("C:\MiKTeX 2.9\tex\generic\oberdiek\ifluatex.sty"))))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\logreq\logreq.sty
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\logreq\logreq.def))
("C:\MiKTeX 2.9\tex\latex\ltxmisc\url.sty")
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\blx-dm.def)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\blx-compat.def)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\biblatex.def)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex-apa\apa.bbx
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\bbx\standard.bb
x)

Package biblatex Warning: Macro 'reviewauthor' undefined.
(biblatex)                Using \newbibmacro.

) (C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex-apa\apa.cbx)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\biblatex.cfg)))
 ("C:\MiKTeX 2.9\tex\latex\tools\enumerate.sty")
("C:\MiKTeX 2.9\tex\latex\hyperref\hyperref.sty"
("C:\MiKTeX 2.9\tex\generic\oberdiek\hobsub-hyperref.sty"
("C:\MiKTeX 2.9\tex\generic\oberdiek\hobsub-generic.sty"))
("C:\MiKTeX 2.9\tex\latex\hyperref\pd1enc.def")
("C:\MiKTeX 2.9\tex\latex\00miktex\hyperref.cfg"))

Package hyperref Message: Driver (autodetected): hpdftex.

("C:\MiKTeX 2.9\tex\latex\hyperref\hpdftex.def"
("C:\MiKTeX 2.9\tex\latex\oberdiek\rerunfilecheck.sty"))
("C:\MiKTeX 2.9\tex\latex\graphics\graphicx.sty"
("C:\MiKTeX 2.9\tex\latex\graphics\graphics.sty"
("C:\MiKTeX 2.9\tex\latex\graphics\trig.sty")
("C:\MiKTeX 2.9\tex\latex\00miktex\graphics.cfg")
("C:\MiKTeX 2.9\tex\latex\pdftex-def\pdftex.def")))
("C:\MiKTeX 2.9\tex\latex\base\textcomp.sty"
("C:\MiKTeX 2.9\tex\latex\base\ts1enc.def"))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\placeins\placeins.sty)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\setspace\setspace.sty)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\appendix\appendix.sty)
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\subfig\subfig.sty)
("C:\MiKTeX 2.9\tex\latex\ams\math\amsmath.sty"
For additional information on amsmath, use the `?' option.
("C:\MiKTeX 2.9\tex\latex\ams\math\amstext.sty"
("C:\MiKTeX 2.9\tex\latex\ams\math\amsgen.sty"))
("C:\MiKTeX 2.9\tex\latex\ams\math\amsbsy.sty")
("C:\MiKTeX 2.9\tex\latex\ams\math\amsopn.sty"))
("C:\MiKTeX 2.9\tex\latex\graphics\color.sty"
("C:\MiKTeX 2.9\tex\latex\00miktex\color.cfg"))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex-apa\american-ap
a.lbx
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\lbx\american.lb
x
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\lbx\english.lbx
)))
("C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final 
paper\example.aux") ("C:\MiKTeX 2.9\tex\latex\base\ts1cmr.fd")
("C:\MiKTeX 2.9\tex\latex\psnfss\ot1ptm.fd")
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
ABD: EverySelectfont initializing macros
("C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final 
paper\example.bbl") ("C:\MiKTeX 2.9\tex\latex\hyperref\nameref.sty"
("C:\MiKTeX 2.9\tex\generic\oberdiek\gettitlestring.sty"))
("C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final 
paper\example.out")
("C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final 
paper\example.out")
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\context\base\supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
)
Underfull \hbox (badness 10000) in paragraph at lines 33--33
 []\OT1/ptm/m/n/12 TITLE 

Underfull \hbox (badness 10000) in paragraph at lines 33--33
 []\OT1/ptm/m/n/12 ME 
("C:\MiKTeX 2.9\tex\latex\psnfss\ot1pcr.fd")
Underfull \hbox (badness 10000) in paragraph at lines 33--33
 \OT1/pcr/b/n/14.4 leavefloats \OT1/ptm/b/n/14.4 op-tion be-fore you sub-mit! 

Underfull \hbox (badness 10000) in paragraph at lines 33--33
 []\OT1/ptm/m/n/12 Author Note 
[1{C:/Users/trinker/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
Underfull \hbox (badness 10000) in paragraph at lines 33--33
 [][]\OT1/ptm/m/n/12 Abstract 
! Undefined control sequence.
\HyOrg@maketitle ... \mspart {Abstract}\@abstract 
                                                  \mspart {\@title }
l.33 \cite
          {Bennett1954}
? 
[2]
Underfull \hbox (badness 10000) in paragraph at lines 33--33
 [][]\OT1/ptm/m/n/12 TITLE 

LaTeX Warning: Citation 'Bennett1954' on page 3 undefined on input line 33.


LaTeX Warning: Citation 'Bennett1954' on page 3 undefined on input line 36.

[3]

LaTeX Warning: Empty bibliography on input line 38.


("C:\Users\trinker\Desktop\PhD Program\CEP 510 Psychometrics\Assignments\Final 
paper\example.aux")

LaTeX Warning: There were undefined references.


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

 )
(\end occurred when \ifx on line 46 was incomplete)
(\end occurred when \ifx on line 46 was incomplete)
(\end occurred when \ifx on line 46 was incomplete){C:/MiKTeX 2.9/fonts/enc/dvi
ps/fontname/8r.enc}<C:/MiKTeX 2.9/fonts/type1/urw/courier/ucrb8a.pfb><C:/MiKTeX
 2.9/fonts/type1/urw/courier/ucrbo8a.pfb><C:/MiKTeX 2.9/fonts/type1/urw/times/u
tmb8a.pfb><C:/MiKTeX 2.9/fonts/type1/urw/times/utmbi8a.pfb><C:/MiKTeX 2.9/fonts
/type1/urw/times/utmr8a.pfb>
Output written on example.pdf (3 pages, 51420 bytes).
SyncTeX written on example.synctex.
Transcript written on example.log.
texify: pdflatex.exe failed for some reason (see log file).


_____________________________________________________________________

 PDFTeXify Compilation Report (Pages: 3)

 Errors: 1   Warnings: 7   Bad Boxes: 6
_____________________________________________________________________

Answer 1

You're one of the first users bitten from the recent update to biblatex, which now uses biber as backend, by default; this is explained in the log file by

Package biblatex Warning: No "backend" specified, using Biber backend.
(biblatex)                To use BibTeX, load biblatex with 
(biblatex)                the "backend=bibtex" option.

So you either use biber instead of BibTeX or say

\usepackage[style=apa,backend=bibtex]{biblatex}

in your preamble.

However, as Audrey comments, style=apa now requires biber as backend. So you should follow the first road:

biber file

instead of

bibtex file

How to launch biber instead of bibtex depends on what you're using as front-end to LaTeX: TeXworks, TeXStudio or whatnot. Without this information it's impossible to suggest more. However, the following discussion

http://old.nabble.com/(pdf)texify-using-biber-instead-of-bibtex-td30017737.html

can help you.

Answer 2

It looks like you're using WinEdt7 and, in particular, the PDFTeXify button (or the very similar PDFLaTeXify button) to compile your file. The PDF(La)TeXify button is very convenient because it'll run LaTeX, BibTeX (if necessary), and MakeIndex (if necessary) however many times are required to get all cross-references and citations fully resolved. However, as you're discovering, the macro that underlies this "button" runs BibTeX by default even though what's really needed for your LaTeX file is biber.

If you are indeed using this PDFTeXify button, you can proceed by modifying one of the WinEdt macro definition files so that the program invokes biber rather than bibtex. Here's what I suggest you do. In the file PDFTeXify.edt (which governs the behavior of the PDFTeXify "button", there's a call to an environment variable named BibTeX-Executable. This variable, in turn, is assigned a value by the instruction

Assign(!"BibTeX-Executable", !|bibtex.exe|); 

on line 280 of the file ExeMode.edt. (On my system, the file ExeMode.edt is located in the directory ..\WinEdt Team\WinEdt7\Exec\Default\ and is dated 2011/05/20. If you have a different file version, the line in question may also be located somewhere else.)

Change this line to

Assign(!"BibTeX-Executable", !|biber.exe|); 

and save the .edt file. You will probably have to exit and restart WinEdt for this change to take effect.

Addendum -- A word of caution: This change of assignment of the BibTeX-Executable environment variable from bibtex.exe to biber.exe is quite likely going to affect many other processes run by WinEdt. If you are not going to be using biblatex (and biber) exclusively, be on the lookout for strange error messages that may be caused by WinEdt trying to run biber when it should be running bibtex instead.

Answer 3

WinEdt uses BibTeX by default, but in your case should use biber. To make WinEdt 7.0 use biber instead of BibTeX, select the "BibTeX" accessory in the Execution Modes window (Options -> Execution Modes) and in the "Command Line" fields at the bottom, change bibtex.exe to biber.exe.

This is also mentioned in the WinEdt help under the entry for "Execution Modes".