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After updating Biber and Biblatex to the latest versions with Tex Live Utility (Mac OS) LaTEX no longer produced any bibliography output. This was likely due to the name formatting changes in Biblatex 3.3. I tried changing all mentions of 'last name' to 'family' and 'first name' to 'given', which then produced an incomplete bibliography that ignored my previous formatting.

@moewe correctly identified that problems in the bib file may be causing trouble in addition to the Biber & BibLatex updates.

Running Biber alone (not PdfLatex) on a limited selection of references produces the following:

Process started

INFO - This is Biber 2.4 INFO - Logfile is 'test1.blg' INFO - Reading 'test1.bcf' INFO - Found 5 citekeys in bib section 0 INFO - Processing section 0 INFO - Looking for bibtex format file '/Users/Sam/Dropbox/PhD/Thesis/Texfiles/LaTexbibliography.bib' for section 0 INFO - Decoding LaTeX character macros into UTF-8 INFO - Found BibTeX data source '/Users/Sam/Dropbox/PhD/Thesis/Texfiles/LaTexbibliography.bib' WARN - BibTeX subsystem: /var/folders/rj/pf22n46x3nj57jynk3h3j66m0000gn/T/YfVI4j5Rr2/LaTexbibliography.bib_2277.utf8, line 17, warning: 457 characters of junk seen at toplevel INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' INFO - Sorting list 'nyt/global' of type 'entry' with scheme 'nyt' and locale 'en-US' INFO - No sort tailoring available for locale 'en-US' INFO - Writing 'test1.bbl' with encoding 'UTF-8' INFO - Output to test1.bbl INFO - WARNINGS: 1

Process exited normally

I have two questions:

  1. Are these warnings important? The true .bib file is much larger. Is there a way to troubleshoot it to identify which other references within it will cause problems?

  2. Despite these warnings, I can produce a functional part document with the bibliography formatted as I'd like. Problems arise when I incorporate a subfile into the main document, despite trying to use code suggested in Bibliographies when using subfiles.

Error messages are

"File ended while scanning use of \field" (compiling the subfile)

or

"File ended while scanning use of \subfile" (compiling the main document)

Have the changes to Biber and BibLatex required changes to the subfile commands, when the subfiles contain references to go in the bibliography of the main file? If so, what should those changes be?

With:

\documentclass[11pt,a4paper,twoside,openright]{book}

\usepackage{subfiles}
\usepackage{filecontents}
% other packages

% Reconcile bibliography processing for subfiles
\makeatletter
\newrobustcmd*{\nobibliography}{%
  \@ifnextchar[%]
    {\blx@nobibliography}
    {\blx@nobibliography[]}}
\def\blx@nobibliography[#1]{}
\appto{\skip@preamble}{\let\printbibliography\nobibliography}
\makeatother

\addbibresource{LaTexbibliography.bib}

%Example for the MWE
% \begin{filecontents}{Chapter1.tex}
% \documentclass[Mainthesis.tex]{subfiles}
% \begin{document}
% Chapter 1 text, citing \parencite{Areference2015}.
% \end{document}
% \end{filecontents}

\begin{document}

\subfiles{Chapter1}

\printbibliography

\end{document}
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leumsa
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    The next one. Check http://tex.stackexchange.com/questions/299036/biblatex-3-3-name-formatting/299084#299084 – Ulrike Fischer Mar 15 '16 at 12:42
  • You definitely have some of the problems explained in Ulrike's link above (namely \mkbibnamelast etc. and \DeclareNameAlias{default}{last-first}). But the Biber error you get should not have to do with that I don't think. I can, however, not reproduce the problem with the (admittedly messy) entry you posted, so there is something else going on in your .bib file (at line 1?). – moewe Mar 15 '16 at 13:24
  • Mhhh, the entry Hurst2008 has some garbage 2006/11/14 09:00 in the middle of the entry. If I get rid of that and cobble the rest together to an MWE I get the expected output with citations and all. – moewe Mar 15 '16 at 13:57
  • Some of the references may have this problem. My issue now is that when I try to build the document from scratch (using the components that were in the subfiles) it ultimately reverts to the same problem with a garbage bibliography and loss of formatting. Bibliographies often start with this: blx@hook@bibinit - does that lead anywhere? – leumsa Mar 15 '16 at 15:25
  • Sorry, without a short example that really reproduces the problem, I can't say much more. Make sure to delete all auxiliary files and try again. Make sure that Biber doesn't choke on your .bib file again, then tackle the LaTeX problem and describe the error message in more detail. – moewe Mar 15 '16 at 16:01
  • Deleting auxiliary files & rerunning hasn't helped, although Biber is processing the bib file to produce a bibliography output (albeit an incorrect one). I'll enter a new example in a bit - unfortunately the error is only reproduced with lengthy preamble code, so it's not that short. – leumsa Mar 15 '16 at 16:07
  • Try and water down the preamble content as much as possible. It would also be great if the example were to work without subfiles and that many included files, a one-file example is really what you should aim for. – moewe Mar 15 '16 at 16:11
  • Make sure Biber is processing without errors or warnings. Sometimes Biber will only issue a warning and plough through heroically even though something went quite horribly wrong in your file. – moewe Mar 15 '16 at 16:12
  • Ad 1: Junk characters at top level need not necessarily be problematic (for example JabRef and I assume other reference managers add some publicity blurb at the beginning of the file which is classed as junk and ignored), but they can indicate another problem (missing braces, commas, ...). Ad 2: Your MWE has some issues, for one it doesn't even load biblatex and it says \subfiles{Chapter1} instead of \subfile. When I changed these obvious problems I got the expected output (I had to use biblatex-examples.bib). – moewe Mar 16 '16 at 07:20
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    Ultimately the problem seemed due to those 2 problems - the biber update, and a rogue reference in the .bib file. Please mark it solved with the comments from @UlrikeFischer – leumsa Mar 17 '16 at 07:23

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