references not printing to pdf properly

Question

I've struggled with a new computer and miktex for sometime. I asked this question before and thought I had it resolved (saw a green hyper link box in the pdf and assumed all was good) but did not. (See question: references not printing). I have some more information and hopefully can get this solved.

I stopped using WinEdt and can replicate the problem in MikTeX.

Here is the code I'm running:

\documentclass[leavefloats]{apa6e}
\usepackage[american]{babel}
\usepackage{csquotes}
%\usepackage[style=apa]{biblatex}
\usepackage[style=apa, backend=biber, bibencoding=latin1]{biblatex}
\addbibresource{explicit.bib}
\DeclareLanguageMapping{american}{american-apa}

\usepackage{enumerate}
\usepackage{hyperref}
\usepackage{graphicx}
\usepackage{ragged2e}
\usepackage{textcomp}
%\usepackage[justification=justified,singlelinecheck=false,font=small,format=plain,labelfont=bf,up,textfont=normal,up]{caption}
\usepackage{etoolbox}
\usepackage{microtype}  %disable ligitures
\DisableLigatures{encoding = *, family = *}

%--------------------------
\makeatletter
\renewcommand{\maketitle}{%
\thispagestyle{titlepage}%
\vspace*{1in}%
\Centering\@title\\\@author%
\vfill%
\ifdefined%
\apaSIXe@leavefloats{}
\fi
\RaggedRight%
\mspart{\@title}%
}
\makeatother
%---------------

\usepackage[section]{placeins}

\usepackage{setspace}
\usepackage{appendix}
\usepackage{float}
\usepackage{subfig}
\usepackage{amsmath}
 %\numberwithin{equation}{subsection} %changes labeling of equations

\setlength{\parindent}{1 em}
\usepackage{color}
\usepackage{ifthen}
\makeatletter
\renewenvironment{figure}[1][]{%
\ifthenelse{\equal{#1}{}}{%
\@float{figure}
}{%
\@float{figure}[#1]%
}%
\centering
}{%
\end@float
}
\renewenvironment{table}[1][]{%
\ifthenelse{\equal{#1}{}}{%
\@float{table}
}{%
\@float{table}[#1]%
}%
\centering
}{%
\end@float
}

\defbibheading{bibliography}{%
\section{\normalfont\refname}}

\title{Teacher Metacognition: The Intentionality of Teacher Led Speech}
\shorttitle{Intentionality of Teacher Led Speech}
\author{Tyler Rinker\\University at Buffalo\\Department of Learning and Instruction}

\authornote{Theories of Language \& Literacy}%LAI 687 -

\date{\today} 
\begin{document}
\maketitle
%\defbibheading{bibliography}{%
%\section{\normalfont\refname}}

%\hspace{.5in}Usually a paper has an introduction but there is no heading for the introduction.  That's what you've got here, an introduction with no heading.  %Not pretty but it pleases the APA.

I want this to work \cite{Nagy1985}

\clearpage %This forces a page break
\printbibliography

\end{document}

I When I run this with both biber and bibtex as the backend. Here is a zip file with my bib file, tex file and the two pdfs that out put using biber and bibtex as backend.

https://dl.dropbox.com/u/61803503/my%20items.zip

Now for some information. If I run it with bibtex as the backend the references never print and the in text citation appears as the bibtex citation key in bold. Ok if I switch to biber as the back end the references still don't print but the in text citation appears correct (green hyper link box around it and the year) but when I click on it it takes me to my cover page as there is no reference section to go to.

If I run the same pdfLatex thing again (the green play button in texworks labeled Typeset if you hover over it) the green intext hyper reference boxes go away and the in text citation is not a date any more but the bold BibTex key instead. The only way to get it back to being green hyper box with year is to switch to bibtex as backend, run it, and the switch back to biber as the back end.

Here is the console out put:

Command Line:   bibtex.exe "theories"
Startup Folder: C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explicit_talk\paper

This is BibTeX, Version 0.99d (MiKTeX 2.9)
The top-level auxiliary file: theories.aux
The style file: biblatex.bst
Database file #1: theories-blx.bib
Database file #2: explicit.bib
Biblatex version: 2.1


Command Line:   texify.exe --pdf --tex-option=--interaction=errorstopmode --tex-option=--synctex=-1 "C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explicit_talk\paper\theories.tex"
Startup Folder: C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explicit_talk\paper

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

("C:/Users/trinker/Desktop/PhD Program/Indep. Study/lit_review_articles_explici
t_talk/paper/theories.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-2012-05-30, greek, gujarati, hindi, hungarian, iceland
ic, indonesian, interlingua, irish, italian, kannada, kurmanji, latin, latvian,
 lithuanian, malayalam, marathi, mongolian, mongolianlmc, monogreek, ngerman, n
german-x-2012-05-30, nynorsk, oriya, panjabi, pinyin, polish, portuguese, roman
ian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, swissgerm
an, tamil, telugu, turkish, turkmen, ukenglish, ukrainian, uppersorbian, usengl
ishmax, 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:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\article.cls"
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\size12.clo"))
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\times.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\mathptmx.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\geometry\geometry.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\graphics\keyval.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\ifpdf.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\ifvtex.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\ifxetex\ifxetex.sty")
("C:\Program Files (x86)\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:\Program Files (x86)\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:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\ifthen.sty"))
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\babel\babel.sty"
*************************************
* Local config file bblopts.cfg used
*
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\arabi\bblopts.cfg)
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\babel\english.ldf"
("C:\Program Files (x86)\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:\Program Files (x86)\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
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\biblatex\biblatex2.sty
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\oberdiek\kvoptions.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\ltxcmds.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\kvsetkeys.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\infwarerr.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\etexcmds.sty"
("C:\Program Files (x86)\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:\Program Files (x86)\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:\Program Files (x86)\MiKTeX 2.9\tex\latex\tools\enumerate.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\hyperref\hyperref.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\hobsub-hyperref.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\hobsub-generic.sty"))
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\hyperref\pd1enc.def")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\00miktex\hyperref.cfg"))

Package hyperref Message: Driver (autodetected): hpdftex.

("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\hyperref\hpdftex.def"
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\oberdiek\rerunfilecheck.sty"))
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\graphics\graphicx.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\graphics\graphics.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\graphics\trig.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\00miktex\graphics.cfg")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\pdftex-def\pdftex.def")))
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\textcomp.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\ts1enc.def"))
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\microtype\microtype.sty
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\microtype\microtype.cfg)
) (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:\Program Files (x86)\MiKTeX 2.9\tex\latex\ams\math\amsmath.sty"
For additional information on amsmath, use the `?' option.
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\ams\math\amstext.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\ams\math\amsgen.sty"))
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\ams\math\amsbsy.sty")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\ams\math\amsopn.sty"))
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\graphics\color.sty"
("C:\Program Files (x86)\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\Indep. Study\lit_review_articles_explici
t_talk\paper\theories.aux")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\ts1cmr.fd")
("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\psnfss\ot1ptm.fd")
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
ABD: EverySelectfont initializing macros

Package biblatex Warning: File 'theories.bbl' is wrong format version - expecte
d 2.1.


("C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explici
t_talk\paper\theories.bbl"
! Undefined control sequence.
<argument> ...c@refsection @entry@\blx@slist@name 

l.119 \endentry

? 
! Undefined control sequence.
<argument> ...c@refsection @entry@\blx@slist@name 

l.119 \endentry

? 
! Undefined control sequence.
l.121 \lossort

? 
! Undefined control sequence.
l.122 \endlossort

? 
) ("C:\Program Files (x86)\MiKTeX 2.9\tex\latex\hyperref\nameref.sty"
("C:\Program Files (x86)\MiKTeX 2.9\tex\generic\oberdiek\gettitlestring.sty"))
("C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explici
t_talk\paper\theories.out")
("C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explici
t_talk\paper\theories.out")
(C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\context\base\supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (C:\Users\trinker\AppData\Roaming\MiKTeX\2.9\tex\latex\microtype\mt-ptm.cfg)
Underfull \hbox (badness 2941) in paragraph at lines 83--83
 []\OT1/ptm/m/n/12 (+20) Teacher Metacog-ni-tion: The In-ten-tion-al-ity of Tea
cher Led Speech 

Underfull \hbox (badness 10000) in paragraph at lines 83--83
 []\OT1/ptm/m/n/12 (+20) Tyler Rinker 

Underfull \hbox (badness 10000) in paragraph at lines 83--83
 []\OT1/ptm/m/n/12 (+20) University at Buf-falo 

Underfull \hbox (badness 10000) in paragraph at lines 83--83
 []\OT1/ptm/m/n/12 (+20) Department of Learn-ing and In-struc-tion 
[1{C:/Users/trinker/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
Underfull \hbox (badness 2922) in paragraph at lines 83--83
 [][]\OT1/ptm/m/n/12 (+20) Teacher Metacog-ni-tion: The In-ten-tion-al-ity of T
eacher Led Speech 

Underfull \hbox (badness 10000) in paragraph at lines 109--109
 [][]\OT1/ptm/b/n/12 Literature Re-view 

Underfull \hbox (badness 10000) in paragraph at lines 118--118
 [][]\OT1/ptm/b/n/12 Methods 

Underfull \hbox (badness 10000) in paragraph at lines 124--124
 [][]\OT1/ptm/b/n/12 Results 

Underfull \hbox (badness 10000) in paragraph at lines 126--126
 [][]\OT1/ptm/b/n/12 Conclusion 
[2]

LaTeX Warning: Empty bibliography on input line 134.


("C:\Users\trinker\Desktop\PhD Program\Indep. Study\lit_review_articles_explici
t_talk\paper\theories.aux")

Package biblatex Warning: Please rerun LaTeX.
(biblatex)                Page breaks have changed.

 )
(\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)pdfTeX warning (dest): name{
cite.0@Nagy1985} has been referenced but does not exist, replaced by a fixed on
e

{C:/Program Files (x86)/MiKTeX 2.9/fonts/enc/dvips/fontname/8r.enc}<C:/Program 
Files (x86)/MiKTeX 2.9/fonts/type1/urw/times/utmb8a.pfb><C:/Program Files (x86)
/MiKTeX 2.9/fonts/type1/urw/times/utmr8a.pfb>
Output written on theories.pdf (2 pages, 35260 bytes).
SyncTeX written on theories.synctex.
Transcript written on theories.log.
texify: pdflatex.exe failed for some reason (see log file).


_____________________________________________________________________

 PDFTeXify Compilation Report (Pages: 2)

 Errors: 4   Warnings: 5   Bad Boxes: 9
_____________________________________________________________________

It still makes a pdf but with no references.

I'm not really that great with LATEX (love it's flexibility but am not really knowledgeable). So please make sure your answers assume nothing.

EDIT: I changed the code and the output above to reflect the problem after trying the solutions given

Answer 1

There are two issues with your files. Firstly, \addbibresource requires the full file name including the extension .bib. Secondly, your bibliography file includes foreign characters in latin1 encoding (e.g. in the French abstract). This means (a) that you need to use a bibliography program that understands such encondings, biber is a good choice, and (b) you need to tell biber about this encoding. This you can do with the option bibencoding=latin1.

Thus, all you really need to do is change two lines in your main file to

\usepackage[style=apa,backend=biber,bibencoding=latin1]{biblatex}
\addbibresource{explicit.bib}

Before trying to compile this, clean out all the generated files from the directory so that you just have your .tex and .bib file left, otherwise you will get all sorts of potentially confusing error messages.