1

Problem fixed: I deleted all log, aux, toc etc and rebuild the file, it works all right and PDF is produced.

I am using LaTeX and template provided by the Uni to formatting my thesis, but I cannot get a bibliography list.

In thesispreamble.tex:

\usepackage[backend=biber,articletitle=true,style=chem-rsc,doi=false]
{biblatex}

In thesis.tex:

\addbibresource{PhylogeneticApproach.bib}
\cleardoublepage
\phantomsection  
\addcontentsline{toc}{chapter}{Bibliography}              
\printbibliography

In the text, I use \textcite and \cite to make citations (this is what I got from the document).

And in Options-Configure TeXstudio-Default Bibliography tool, I changed Bibtex to Biber.

However, I cannot get any bibliography list.

Is there any solution? Thanks in advance.

Edit: TeXstudio produces numerous errors after build& view -biber-build & view and cannot produce PDF, the following is the log file (I deleted part of them):

line 21: File ended while scanning use of \field. \begin{document}
line 4: Missing number, treated as zero. ...allenges faced by banks \textcite{Lin2013}
line 4: Missing number, treated as zero. ...allenges faced by banks \textcite{Lin2013}
line 4: Missing number, treated as zero. ...allenges faced by banks \textcite{Lin2013}
line 39: Undefined control sequence. \begin{quotation}
line 45: Undefined control sequence. \begin{quotation}
line 53: Undefined control sequence. \begin{quotation}
line 64: Undefined control sequence. \begin{quotation}
line 272: Undefined control sequence. \begin{quotation}
line 36: Undefined control sequence. \begin{quotation}
line 42: Undefined control sequence. \begin{quotation}
line 74: Missing \endcsname inserted.
line 74: Undefined control sequence.
line 74: Missing \endcsname inserted.
line 74: Undefined control sequence.
line 74: Extra \fi.
line 74: Missing number, treated as zero.
line 74: Illegal unit of measure (pt inserted).
line 74: Extra \endcsname.
line 74: Extra \endcsname.
line 74: Use of \expandafter doesn't match its definition.
line 74: Missing { inserted.
line 74: Argument of \renew@command has an extra }.
line 74: Paragraph ended before \renew@command was complete.
line 74: Extra }, or forgotten \endgroup.
line 74: Argument of \makelabel has an extra }.
line 74: Paragraph ended before \makelabel was complete.
line 74: You can't use `macro parameter character #' in horizontal mode.

......

line 74: Undefined control sequence.
line 74: Use of expandafter doesn't match its definition.
line 74: Use of expandafter doesn't match its definition.
line 74: Use of noexpand doesn't match its definition.
line 2: Use of expandafter doesn't match its definition. [2001/06/04 font definitions for OT1/ptm.]
line 4: Use of expandafter doesn't match its definition. \DeclareFontFamily{OT1}{ptm}{}
line 4: Use of expandafter doesn't match its definition. \DeclareFontFamily{OT1}{ptm}{}
line 4: Encoding scheme `OT1' unknown. \DeclareFontFamily{OT1}{ptm}{}
line 4: Use of expandafter doesn't match its definition. \DeclareFontFamily{OT1}{ptm}{}
line 4: Use of expandafter doesn't match its definition. \DeclareFontFamily{OT1}{ptm}{}
line 6: Missing endcsname inserted. \DeclareFontShape
line 6: You can't use a prefix with `begingroup'. \DeclareFontShape
line 6: Use of expandafter doesn't match its definition. \DeclareFontShape
line 8: Use of expandafter doesn't match its definition. }{}
line 8: Font family `OT1+ptm' unknown. }{}

......

: No \title specified!.
: No \author specified!.
: No \degree specified!.
: No \supervisor specified!.
: No \school specified!.
: No \author specified!.
: No \author specified!.
: No \degree specified!.
: No \author specified!.
line 12: Citation 'EnglandPrudentialRegulationAuthority2015' on page 1 undefined
line 11: Overfull \hbox (67.95175pt too wide) in paragraph
: pdflatex.exe (file ./figures/chap2intro.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed<figures/chap2intro.pdf, id=354, 507.39563pt x 404.26031pt>File: figures/chap2intro.pdf Graphic file (type pdf)
line 29: Overfull \hbox (5.0141pt too wide) in paragraph
line 31: Citation 'Abbott1988' on page 4 undefined

: No positions in optional float specifier.
: No positions in optional float specifier.
line 669: Overfull \hbox (69.7424pt too wide) in paragraph
line 703: Reference `appendfig:HEU2008-2010' on page 59 undefined
line 703: Reference `appendfig:HEU2013-2014' on page 59 undefined
line 703: Reference `append8' on page 59 undefined
: No positions in optional float specifier.
: No positions in optional float specifier.
line 744: Overfull \hbox (69.7424pt too wide) in paragraph
line 803: Underfull \hbox (badness 2334) in paragraph
line 803: Underfull \hbox (badness 4660) in paragraph
: pdflatex.exe (file ./figures/chap6intro.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed<figures/chap6intro.pdf, id=1051, 227.34938pt x 368.1253pt>File: figures/chap6intro.pdf Graphic file (type pdf)

......

: No positions in optional float specifier.
line 21: Citation 'Ganegoda2013' on page 70 undefined
line 21: Citation 'Sturm2013' on page 70 undefined
line 21: Citation 'Fiordelisi2014' on page 70 undefined
: Overfull \hbox (244.5006pt too wide) has occurred while \output is active
: Overfull \hbox (244.5006pt too wide) has occurred while \output is active

The following is the thesis.blg file:

[0] Config.pm:354> INFO - This is Biber 2.7
[0] Config.pm:357> INFO - Logfile is 'thesis.blg'
[36] biber-MSWIN64:303> INFO - === 
[77] Biber.pm:359> INFO - Reading 'thesis.bcf'
[188] Biber.pm:835> INFO - Found 171 citekeys in bib section 0
[204] Biber.pm:3670> INFO - Processing section 0
[223] Biber.pm:3840> INFO - Looking for bibtex format file 
'PhylogeneticApproach.bib' for section 0
[322] bibtex.pm:1435> INFO - Decoding LaTeX character macros into UTF-8
[496] bibtex.pm:1292> INFO - Found BibTeX data source 
'PhylogeneticApproach.bib'
[611] Utils.pm:164> WARN - month field '1/1/2007' in entry 'Allen2007' is 
not an integer - this will probably not sort properly.
[618] Utils.pm:164> WARN - ISBN '9780470481806 0470481803' in entry 
'Malz2011' is invalid - run biber with '--validate_datamodel' for details.
[622] Utils.pm:164> WARN - month field 'December 2000' in entry 'Tripe2000' 
is not an integer - this will probably not sort properly.
[623] Utils.pm:164> WARN - Name "Galai D., Ruthenberg D., Sarnat M., 
Schreiber B.Z." has too many commas: skipping name
[647] Utils.pm:164> WARN - month field '1/1/2002' in entry 'Hillson2002' is 
not an integer - this will probably not sort properly.
[678] Utils.pm:164> WARN - ISBN '978-0195157215 0195157214' in entry 
'Park2005' is invalid - run biber with '--validate_datamodel' for details.
[681] Utils.pm:164> WARN - ISBN '0415152860 0415152879' in entry 
'Cilliers1998' is invalid - run biber with '--validate_datamodel' for 
details.
[687] Utils.pm:164> WARN - month field '1/1/2006' in entry 'Mitchell2006' is 
not an integer - this will probably not sort properly.
[699] Utils.pm:164> WARN - month field '1/1/2007' in entry 'Marwan2007' is 
not an integer - this will probably not sort properly.
[702] Utils.pm:164> WARN - ISBN '9780684868769 0684868768 9780684868752 
068486875x' in entry 'Johnson2004' is invalid - run biber with '--
validate_datamodel' for details.
[704] Utils.pm:164> WARN - month field '1997/01/01' in entry 'Dooley1997' is 
not an integer - this will probably not sort properly.
[705] Utils.pm:164> WARN - ISBN '0195058119 0195079515' in entry 
'Kauffman1993' is invalid - run biber with '--validate_datamodel' for 
details.
[725] Utils.pm:164> WARN - month field '1/1/2005' in entry 'Chen2005' is not 
an integer - this will probably not sort properly.
[753] Utils.pm:164> WARN - ISBN '978���0���19���933829���0 
978���0���19���933830���6' in entry 'Diebold2015' is invalid - run 
biber with '--validate_datamodel' for details.
[755] Utils.pm:164> WARN - month field '08//' in entry 'Neil2005' is not an 
integer - this will probably not sort properly.
[759] Utils.pm:164> WARN - month field 'Spring Spring 2009 2012-01-26' in 
entry 'Neil2009' is not an integer - this will probably not sort properly.
[780] Utils.pm:164> WARN - month field '1/1/1999' in entry 'Barabasi1999' is not an integer - this will probably not sort properly.
[782] Utils.pm:164> WARN - month field '1/1/2005' in entry 'Garlaschelli2005' is not an integer - this will probably not sort properly.
[787] Utils.pm:164> WARN - month field '1972/01/01' in entry 'Bonacich1972a' is not an integer - this will probably not sort properly.
[792] Utils.pm:164> WARN - month field 'Nov' in entry 'Foster2005' is not an integer - this will probably not sort properly.
[797] Utils.pm:164> WARN - month field '3 Dec 2015' in entry 'Evans2015' is not an integer - this will probably not sort properly.
[806] Utils.pm:164> WARN - month field '4/1/April 2016' in entry 'Danielsson2016' is not an integer - this will probably not sort properly.
[846] Utils.pm:164> WARN - month field '10/21/' in entry 'Kolaczkowski2004' is not an integer - this will probably not sort properly.
[856] Utils.pm:164> WARN - ISBN '978-3-540-32474-1' in entry 'Henke2007' is invalid - run biber with '--validate_datamodel' for details.
[863] Utils.pm:164> WARN - month field '10//' in entry 'Sharifi2016' is not an integer - this will probably not sort properly.
[871] Utils.pm:164> WARN - BibTeX subsystem: C:\Users\speed\AppData\Local\Temp\hlhreN78NQ\PhylogeneticApproach.bib_115836.utf8, line 4, warning: 9 characters of junk seen at toplevel
[974] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
[974] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
[974] Biber.pm:3499> INFO - Sorting list 'none/global/' of type 'entry' with scheme 'none' and locale 'en-US'
[975] Biber.pm:3505> INFO - No sort tailoring available for locale 'en-US'
[1081] bbl.pm:608> INFO - Writing 'thesis.bbl' with encoding 'ascii'
[1086] Utils.pm:164> WARN - The entry 'Kaplan1981' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1087] Utils.pm:164> WARN - The entry 'Allen2007' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1093] Utils.pm:164> WARN - The entry 'Buchmueller2006' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1096] Utils.pm:164> WARN - The entry 'Hillson2002' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1097] Utils.pm:164> WARN - The entry 'Kaiser2006' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1099] Utils.pm:164> WARN - The entry 'Scandizzo2005' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1102] Utils.pm:164> WARN - The entry 'Singh2010' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1105] Utils.pm:164> WARN - The entry 'Walters2003' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1108] Utils.pm:164> WARN - The entry 'Mauboussin2002' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1111] Utils.pm:164> WARN - The entry 'Sornette2003a' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1113] Utils.pm:164> WARN - The entry 'Barabasi2000' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1116] Utils.pm:164> WARN - The entry 'Mitchell2006' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1121] Utils.pm:164> WARN - The entry 'Marwan2007' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1125] Utils.pm:164> WARN - The entry 'Nishimori2011' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1126] Utils.pm:164> WARN - The entry 'Sole1996' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1127] Utils.pm:164> WARN - The entry 'Sole2011' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1128] Utils.pm:164> WARN - The entry 'Anderson1995' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1130] Utils.pm:164> WARN - The entry 'Chen2005' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1132] Utils.pm:164> WARN - The entry 'Sornette1997' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1134] Utils.pm:164> WARN - The entry 'Pisarenko2003' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1136] Utils.pm:164> WARN - The entry 'Boffetta1999' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1138] Utils.pm:164> WARN - The entry 'Stumpf2012' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1141] Utils.pm:164> WARN - The entry 'Clauset2009' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1144] Utils.pm:164> WARN - The entry 'Billio2013' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1145] Utils.pm:164> WARN - The entry 'Diebold2015' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1147] Utils.pm:164> WARN - The entry 'Neil2005' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1152] Utils.pm:164> WARN - The entry 'Neil2009' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1154] Utils.pm:164> WARN - The entry 'Erdoes1959' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1155] Utils.pm:164> WARN - The entry 'Albert1999' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1156] Utils.pm:164> WARN - The entry 'Erdoes1960' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1159] Utils.pm:164> WARN - The entry 'Baum2003' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1160] Utils.pm:164> WARN - The entry 'Barabasi1999a' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1161] Utils.pm:164> WARN - The entry 'Barabasi1999' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1164] Utils.pm:164> WARN - The entry 'Garlaschelli2005' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1170] Utils.pm:164> WARN - The entry 'Danielsson2002' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1172] Utils.pm:164> WARN - The entry 'Danielsson2008a' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1174] Utils.pm:164> WARN - The entry 'Danielsson2016' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1177] Utils.pm:164> WARN - The entry 'Griffiths1974' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1189] Utils.pm:164> WARN - The entry 'Jobst2007' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1194] Utils.pm:164> WARN - The entry 'Tandon2017' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.
[1195] bbl.pm:712> INFO - Output to thesis.bbl
[1200] Biber.pm:109> INFO - WARNINGS: 66
  • 2
    The error log shows that you are running BibTeX on your file, while backend=biber requires you to run Biber on it instead. See Biblatex with Biber: Configuring my editor to avoid undefined citations for help on letting TeXmaker run Biber for you. – moewe Oct 12 '17 at 15:11
  • BTW: You won't need \cleardoublepage\phantomsection\addcontentsline{toc}{chapter}{Bibliography} if you use \printbibliography[heading=bibnumbered] – moewe Oct 12 '17 at 15:12
  • 1
    To me it seems as if you used \addbibresource after \begin{document}. According to the biblatex documentation this command is only available in the preamble. – leandriis Oct 12 '17 at 15:14
  • If you have already properly set up your editor for Biber (check with the link I gave), you need to be a bit more specific about what does not work for you. What do you see, what do you expect instead? Do you get any errors or warning in the .blg file (Windows classifies it as 'performance monitor file', but it is really only a text file you can open with your favourite editor) - if you don't see a .blg file Biber did not run. Do you get any errors in the .log file? Have a look at Troubleshooting for biber – moewe Oct 12 '17 at 15:16
  • Thanks @moewe, I am using biber, and I edited the post as it make confusions. It doesn't work, I will post the .blg log. Thanks @ leandriis, the \addbibresource is before \begin{document}. – S.Lee Oct 13 '17 at 3:01
2

It seems that you have the error (created with a wrong \addbibresource {\jobname.bib} in line 67)

! LaTeX Error: Can be used only in preamble.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              

l.67 \addbibresource
                    {\jobname.bib} % <=======================================
Your command was ignored.
Type  I <command> <return>  to replace it with another command,
or  <return>  to continue without it.

That means you should move the command \addbibresource {\jobname.bib} into the preamble.

Please see the following MWE (package filecontents is only used to have the bib file and the TeX code in one MWE!) mwe.tex:

\RequirePackage{filecontents}
\begin{filecontents}{\jobname.bib}
@article{einstein,
  author   = "Albert Einstein",
  title    = "{Zur Elektrodynamik bewegter K{\"o}rper}. ({German})
               [{On} the electrodynamics of moving bodies]",
  journal  = "Annalen der Physik",
  volume   = "322",
  number   = "10",
  pages    = "891--921",
  year     = "1905",
  DOI      = "http://dx.doi.org/10.1002/andp.19053221004",
  keywords = "physics",
}
@book{dirac,
  title     = {The Principles of Quantum Mechanics},
  author    = {Paul Adrien Maurice Dirac},
  isbn      = {9780198520115},
  series    = {International series of monographs on physics},
  year      = {1981},
  publisher = {Clarendon Press},
  keywords  = {physics},
}
@Book{goossens,
  author    = {Goossens, Michel and Mittelbach, Frank and
               Samarin, Alexander},
  title     = {The LaTeX Companion},
  edition   = {1},
  publisher = {Addison-Wesley},
  location  = {Reading, Mass.},
  year      = {1994},
}
@Book{adams,
  title     = {The Restaurant at the End of the Universe},
  author    = {Douglas Adams},
  series    = {The Hitchhiker's Guide to the Galaxy},
  publisher = {Pan Macmillan},
  year      = {1980},
}
\end{filecontents}


\documentclass[12pt]{article}

\usepackage[utf8]{inputenc} 
\usepackage[T1]{fontenc} 

\usepackage{csquotes}
\usepackage[%
  backend=biber,
  articletitle=true,
  style=chem-rsc,
  doi=false
]{biblatex}
\addbibresource{\jobname.bib} % <========================== okay! ======


\begin{document}

\tableofcontents

\section{Introduction}
Add \nocite{*} to call all bib entrys or cite at last one 
like~\cite{adams} or~\textcite{goossens}.

%\addbibresource{\jobname.bib} % <======================= wrong!!=======
%\phantomsection  
%\addcontentsline{toc}{chapter}{Bibliography} 
\printbibliography[heading=bibnumbered] % <=============================

\end{document}

and the resulting pdf (compiled without errors and only one warning, comming from filecontents (okay)):

resulting bibliography

If you editor does not show resulting error messages and warnings check the files mwe.log and mwe.blg for errors and warnings.

EDIT:

Your next step can be to validate your bib file.

  • Copy my file mwe.tex to your computer, compile it three times and check that there are no errors.

  • Now copy your first bib entry from file PhylogeneticApproach.bib to the bib file in mwe.tex, compile three times and check for errors and warnings.

  • Correct them. Recompile three times and check for errors ...

  • copy the second bib entry from file PhylogeneticApproach.bib ...

  • ...

  • Thanks, I have tried to move \addbibresource {\jobname.bib} into the preamble but it still not working. – S.Lee Oct 13 '17 at 6:56
  • 2
    @S.Lee "Not working" is not very helpful ... Please check both log files .log and .blg for error messages and add the complete first one to your question! Add the bib entrys for Allen2007, Tripe2000 and Diebold2015 to your question. – Mensch Oct 13 '17 at 9:36
  • Thanks, problem fixed. It is some unkown error to me, but finally I got it done. – S.Lee Oct 15 '17 at 12:02

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.