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The Problem:

When using bibtex as the backend in biblatex, my document compiles as expected. Unfortunately, when I switch to biber, I see the following error:

Citation 'XXX' on page XX undefined on input line XX.

I believe I have imported my references correctly in a .bib format (exported directly from Mendeley). The bibliographies for each chapter and the citations parse correctly when using bibtex as the backend, so my question is:

How can I prevent biber triggering this error?


The Setup:

I am running Overleaf, using the pdfLaTeX compiler and biblatex as my citation package.

I am writing a thesis, so wish to include a bibliography in each separate chapter.


Relevant Code

Preamble Code: This is the relevant section of code that I use to define the citation and bibliography settings in the preamble.

\usepackage[style=nature,
   backend   =biber,
   refsection=chapter,
   intitle   =true,
   sorting   =none,
   giveninits=true,
   citestyle =nature,
   abbreviate=true,
   natbib    =false,
   uniquename=false,
   uniquelist=false,
   date      =year,
   url       =false,
   doi       =false,
   isbn      =false,
   backref   =false,
   hyperref  =auto,
   mincitenames=1,
   maxcitenames=3]{biblatex}
\addbibresource{references.bib}

Citation Code: This is the code I use to make a citation and print the bibliography in each chapter of the document.

\chapter{ChapterTitle} 
Lorem Ipsum \cite{citationkey1}
Lorem Ipsum \cite{citationkey2}

\printbibliography[heading=subbibintoc,title={Bibliography}]

.blg Output File from the Relevant Chapter:

This is BibTeX, Version 0.99d (TeX Live 2021)
Capacity: max_strings=200000, hash_size=200000, hash_prime=170003
The top-level auxiliary file: output3-blx.aux
The style file: biblatex.bst
This database file appears more than once: references.bib
---line 11 of file output3-blx.aux
 : \bibdata{output-blx,references,references
 :                                          }
I'm skipping whatever remains of this command
Reallocated glb_str_ptr (elt_size=4) to 20 items from 10.
Reallocated global_strs (elt_size=200001) to 20 items from 10.
Reallocated glb_str_end (elt_size=4) to 20 items from 10.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated wiz_functions (elt_size=4) to 6000 items from 3000.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Database file #1: output-blx.bib
Database file #2: references.bib
I was expecting a `,' or a `}'---line 6936 of file references.bib
 : 
 : @article{Liu2018TopographicalAnalysis,
(Error may have been on previous line)
I'm skipping whatever remains of this entry
Biblatex version: 3.16
Reallocated wiz_functions (elt_size=4) to 9000 items from 6000.
Reallocated singl_function (elt_size=4) to 100 items from 50.
You've used 1 entry,
            6393 wiz_defined-function locations,
            1201 strings with 8967 characters,
and the built_in function-call counts, 1522 in all, are:
= -- 72
> -- 70
< -- 1
+ -- 49
- -- 28
* -- 31
:= -- 368
add.period$ -- 0
call.type$ -- 1
change.case$ -- 0
chr.to.int$ -- 42
cite$ -- 0
duplicate$ -- 11
empty$ -- 103
format.name$ -- 0
if$ -- 322
int.to.chr$ -- 0
int.to.str$ -- 0
missing$ -- 0
newline$ -- 20
num.names$ -- 0
pop$ -- 47
preamble$ -- 1
purify$ -- 0
quote$ -- 0
skip$ -- 77
stack$ -- 0
substring$ -- 151
swap$ -- 1
text.length$ -- 20
text.prefix$ -- 0
top$ -- 1
type$ -- 22
warning$ -- 0
while$ -- 64
width$ -- 0
write$ -- 20
(There were 2 error messages)

Relevant Reading

Helpful primer on citations packages for LaTeX: bibtex vs. biber and biblatex vs. natbib

Further details on biblatex compatibility: Compatibility of bibtex and biblatex bibliography files?

BibLaTeX Documentation: https://www-uxsup.csx.cam.ac.uk/pub/tex-archive/macros/latex/contrib/biblatex/doc/biblatex.pdf

7
  • 2
    Show the content of the blg-file. Mar 26 at 21:31
  • Maybe a good start to test debugging: tex.meta.stackexchange.com/questions/4407 Mar 26 at 22:21
  • Biber can be a bit more fussy than BibTeX and may throw an error where BibTeX only threw a warning or may even completely abort compilation where BibTeX would error and go on. Any issues that Biber encounters are logged in the .blg file. Please download the .blg file as described in tex.stackexchange.com/q/462314/35864 for the .bbl and add its complete contents to the question (despite what a Windows system may tell you the .blg file is a simple text file you can open with any text editor).
    – moewe
    Mar 27 at 4:16
  • Related tex.stackexchange.com/q/286706/35864.
    – moewe
    Mar 27 at 4:17
  • @moewe - I've now inputted the .blg file with the question.
    – Triz
    Mar 27 at 10:05

1 Answer 1

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Variations in Error Handling: Biber vs. BibTeX

As pointed out by @moewe in the comments on the original question, Biber can be more fussy than BibTeX when handling errors. In this case, this meant that the pdf would compile as intended (including the bibliography) when run with BibTeX, but would compile without the bibliography with Biber.

To troubleshoot this, download the .blg file from the output logs. This will highlight any errors in the .bib file. In this case, there was an additional { in the title of one reference, which caused issues when this was parsed by the Biber backend.

2
  • Fuzziness does not really have anything to do with whether or not a pdf is created. Overleaf compiles documents in a way that generates a pdf regardless of errors (only in certain circumstances the pdf will not be created). As bibtex/biber is external from latex, this is even more true.
    – daleif
    Mar 27 at 12:08
  • Additionally, I'm wondering a bit about your overleaf setup as OL compiles via latexmk which normally picks up the need for biber automatically (I use it on my own pc all the time, great tool)
    – daleif
    Mar 27 at 12:09

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