1

I am trying to ge the same output PDF of a report on MacOS Sierra 10.13.6 and Debian 8 (pdfTex 3.14159265-2.6-1.40.19) with the following commands :

pdflatex rapport_m2
biber rapport_m2
biber rapport_m2
pdflatex rapport_m2
pdflatex rapport_m2

My issue is that I can't have references on Debian OS, I get "undefined references" unlikely on MaOS where I get all valid references (I talk about the bibliography).

You can see the log of compilation for both version :

log compilation on Debian

log compilation on MacOS

The number of pages generated is also different (39 pages on MacOS and only 37 on Debian).

Here is below all the header of my .texreport with all options and packages :

article{Hamilton_1998,
  author = {{Hamilton}, A.~J.~S.},
  title = {{Linear Redshift Distortions: a Review}},
  booktitle = {The Evolving Universe},
  year = {1998},
  editor = {{Hamilton}, D.},
  volume = {231},
  series = {Astrophysics and Space Science Library},
  pages = {185},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
  adsurl = {http://adsabs.harvard.edu/abs/1998ASSL..231..185H},
  bdsk-url-1 = {http://dx.doi.org/10.1007/978-94-011-4960-0_17},
  doi = {10.1007/978-94-011-4960-0_17},
  eprint = {astro-ph/9708102}
}
\end{filecontents}

%\documentclass[11pt,french,oneside]{report}
%\usepackage[utf8]{inputenc}
%\usepackage[T1]{fontenc}
%\usepackage[francais]{babel}
%\usepackage[style=ext-authoryear, backend=biber]{biblatex}
%\usepackage{hyperref}

\documentclass[11pt,french,oneside]{report}
\usepackage[latin1]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[francais]{babel}
\usepackage{indentfirst}
\usepackage{lastpage}
\usepackage{amsmath,amssymb}
\usepackage{fancyhdr}
\usepackage{url}
\usepackage{epsfig}
\usepackage{graphics}
\usepackage{multirow}
\usepackage{vmargin}
\usepackage{float}
\usepackage{psboxit,pstcol}
\usepackage{tabularx}
%\usepackage[style=authoryear]{biblatex}
%\usepackage{biblatex}
%\usepackage[backend=biber,style=authoryear]{biblatex}
\usepackage[style=ext-authoryear, backend=biber]{biblatex}
\usepackage[hyperfootnotes=false,colorlinks,allcolors=blue]{hyperref}
\usepackage[nameinlink,noabbrev]{cleveref}
\Crefname{appendix}{l'Appendice}{les Appendices}
\usepackage{setspace}
\usepackage{needspace}
\usepackage{caption}

%\usepackage{hyperref}
%\usepackage[nameinlink,noabbrev]{cleveref}

\renewcommand*{\bibfont}{\small}

% Default fixed font does not support bold face
\DeclareFixedFont{\ttb}{T1}{txtt}{bx}{n}{9} % for bold
\DeclareFixedFont{\ttm}{T1}{txtt}{m}{n}{9}  % for normal

% Custom colors
\usepackage{color}
\definecolor{deepblue}{rgb}{0,0,0.5}
\definecolor{deepred}{rgb}{0.6,0,0}
\definecolor{deepgreen}{rgb}{0,0.5,0}

\usepackage{listings}

% Python style for highlighting
\newcommand\pythonstyle{\lstset{
language=Python,
basicstyle=\ttm,
otherkeywords={self},             % Add keywords here
keywordstyle=\ttb\color{deepblue},
emph={MyClass,__init__},          % Custom highlighting
emphstyle=\ttb\color{deepred},    % Custom highlighting style
stringstyle=\color{deepgreen},
frame=tb,                         % Any extra options here
showstringspaces=false,
%commentstyle=\fontseries{lc}\selectfont\itshape,columns=fullflexible], 
commentstyle=\ttb\selectfont\itshape,columns=fullflexible], 
numbers=left,
stepnumber=1,
}}


% Python environment
\lstnewenvironment{python}[1][]
{
\pythonstyle
\lstset{#1}
}
{}

% Python for external files
\newcommand\pythonexternal[2][]{{
\pythonstyle
\lstinputlisting[#1]{#2}}}

\DefineBibliographyExtras{french}{\restorecommand\mkbibnamefamily}

\setlength\bibitemsep{\baselineskip}

\addbibresource{\jobname.bib}

\renewcommand*{\nameyeardelim}{\addcomma\space}

\newcommand*{\x}{\mathsf{x}\mskip1mu}

\DeclareCiteCommand{\cite}[\mkbibparens]
  {\usebibmacro{prenote}}
  {\usebibmacro{citeindex}%
   \printtext[bibhyperref]{\usebibmacro{cite}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

\DeclareCiteCommand*{\cite}[\mkbibparens]
  {\usebibmacro{prenote}}
  {\usebibmacro{citeindex}%
   \printtext[bibhyperref]{\usebibmacro{citeyear}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

\newcommand{\emptysection}[1]{%
    \begingroup\renewcommand\addcontentsline[3]{}%
    \section{#1}\endgroup%
}

\makeatletter
\newlength{\chapter@number@width}
\def\@makechapterhead#1{%
  {\normalfont
  \setlength{\parindent}{0pt}%
  \vspace*{10pt}%
  \settowidth{\chapter@number@width}{%
    \hbox{\color{white}\LARGE\bfseries
          \hspace{\dimexpr 1mm+3pt}%
          \thechapter
          \hspace{\dimexpr 1mm+3pt}%
    }}
  \hbox{%
    \vtop{%
      \hsize=\dimexpr\chapter@number@width+\tabcolsep+2\fboxrule+\tabcolsep
      \begin{tabular}[t]{@{}c}
        \scshape\strut\makebox[0pt]{\hspace{0pt plus 1 fill minus 1 fill}\@chapapp\hspace{0pt plus 1 fill minus 1 fill}} \\
        \fboxsep=0pt
        \colorbox{black}{\vbox{%
           \hbox{\vbox to \dimexpr 1mm+3pt{}}
           \hbox{\color{white}\LARGE\bfseries
                 \hspace{\dimexpr 1mm+3pt}%
                 \thechapter
                 \hspace{\dimexpr 1mm+3pt}%
                }
           \hrule height 0.4pt depth 0pt width 0pt
           \hbox{\vbox to 6pt{}}
           \hbox{\parbox{0pt}{\Huge\bfseries\vphantom{E}}}
           }}%
      \end{tabular}%
      }%
    \vtop{%
      \advance\hsize by -\dimexpr\chapter@number@width+2\fboxrule+\tabcolsep
      \hspace*{-0.5cm}\begin{tabular}[t]{c}
        \scshape\strut\vphantom{\@chapapp} \\
        \fboxsep=0pt
        \colorbox{white}{\vbox{%
           \hbox{\vbox to \dimexpr 1mm+3pt{}}
           \hbox{\LARGE\bfseries
                 \hspace{\dimexpr 1mm+3pt}%
                 \phantom{\thechapter}
                 \hspace{\dimexpr 1mm+3pt}%
                }
           \hrule height 0.4pt depth 0pt width \hsize
           \hbox{\vbox to 6pt{}}
           \hbox{\hspace*{20pt}\parbox{\dimexpr\textwidth-2mm-6pt-\chapter@number@width-\tabcolsep-2\fboxrule-20pt}{\Huge\bfseries #1}}
           }}%
      \end{tabular}%
      }%
    }%
  \vspace{50pt}%
  }
}
\def\@makeschapterhead#1{%
  {\normalfont
  \setlength{\parindent}{0pt}%
  \vspace*{10pt}%
  \settowidth{\chapter@number@width}{%
    \hbox{\color{white}\LARGE\bfseries
          \hspace{\dimexpr 1mm+3pt}%
          \thechapter
          \hspace{\dimexpr 1mm+3pt}%
    }}
  \hbox{%
    \vtop{%
      \hsize=\dimexpr\chapter@number@width+\tabcolsep+2\fboxrule+\tabcolsep
      \begin{tabular}[t]{@{}c}
        \scshape\strut\makebox[0pt]{\hspace{0pt plus 1 fill minus 1 fill}\phantom{\@chapapp}\hspace{0pt plus 1 fill minus 1 fill}} \\
        \fboxsep=0pt
        \colorbox{black}{\vbox{%
           \hbox{\vbox to \dimexpr 1mm+3pt{}}
           \hbox{\color{white}\LARGE\bfseries
                 \hspace{\dimexpr 1mm+3pt}%
                 \phantom{\thechapter}%
                 \hspace{\dimexpr 1mm+3pt}%
                }
           \hrule height 0.4pt depth 0pt width 0pt
           \hbox{\vbox to 6pt{}}
           \hbox{\parbox{0pt}{\Huge\bfseries\vphantom{E}}}
           }}%
      \end{tabular}%
      }%
    \vtop{%
      \advance\hsize by -\dimexpr\chapter@number@width+2\fboxrule+\tabcolsep
      \hspace*{-0.5cm}\begin{tabular}[t]{c}
        \scshape\strut\vphantom{\@chapapp} \\
        \fboxsep=0pt
        \colorbox{white}{\vbox{%
           \hbox{\vbox to \dimexpr 1mm+3pt{}}
           \hbox{\LARGE\bfseries
                 \hspace{\dimexpr 1mm+3pt}%
                 \phantom{\thechapter}
                 \hspace{\dimexpr 1mm+3pt}%
                }
           \hrule height 0.4pt depth 0pt width \hsize
           \hbox{\vbox to 6pt{}}
           \hbox{\hspace*{20pt}\parbox{\dimexpr\textwidth-2mm-6pt-\chapter@number@width-\tabcolsep-2\fboxrule-20pt}{\Huge\bfseries #1}}
           }}%
      \end{tabular}%
      }%
    }%
  \vspace{50pt}%
  }
}

\setlength\parindent{0pt}

%%%% debut macro pour changer les marges localement %%%%
\newenvironment{changemargin}[2]{\begin{list}{}{%
\setlength{\topsep}{0pt}%
\setlength{\leftmargin}{0pt}%
\setlength{\rightmargin}{0pt}%
\setlength{\listparindent}{\parindent}%
\setlength{\itemindent}{\parindent}%
\setlength{\parsep}{0pt plus 1pt}%
\addtolength{\leftmargin}{#1}%
\addtolength{\rightmargin}{#2}%
}\item }{\end{list}}
%%%% fin macro %%%%

%\setmarginsrb{2.3cm}{0.3cm}{2.1cm}{1cm}{0.55cm}{1cm}{1cm}{1cm}
\setmarginsrb{2.3cm}{0.0cm}{2.1cm}{1cm}{1.3cm}{0.5cm}{0.4cm}{1cm}
\pagestyle{fancy}
\renewcommand{\footrulewidth}{0.4pt}
\renewcommand{\headrulewidth}{0.4pt}
\chead{\hspace{-0.3cm}\textit{Rapport \hspace{-0.3cm}}}
\lhead{\epsfig{file=logo_sdc_small.jpg,height=1cm,width=2cm}}
\rhead{\epsfig{file=logo_par3_small.png,height=1cm,width=2cm}}
\lfoot{\textit{christian joe}}
\cfoot{\hspace{1.6cm} \textit{ - \'etude des mat\'eriaux - }} 
\rfoot{\thepage/\pageref{LastPage}}

\makeatletter
\g@addto@macro\appendix{%
  \cleardoublepage
  \hypertarget{appendixstart}{}%
  \addtocontents{toc}{
    \protect\contentsline{chapter}{\protect\hyperlink{appendixstart}{Appendice}}{}{}%
  }%
}
\makeatother

\usepackage[nameinlink,noabbrev]{cleveref}

\renewcommand{\arraystretch}{1.25} 

\begin{document}

I apply references by writting : \autocite{2009MNRAS.399.2107K}

Unfortunately, on Debian OS, I can't get to have the references displayed correctly, I have just the name appearing in \autocite{name}.

From all these, informations anyone could tell me where the problem comes from, I mean why this difference between the ouput of the 2 OS ?

UPDATE 1: Indeed, this a problem with biberand this following message :

Output written on rapport_m2.pdf (37 pages, 1289330 bytes).
Transcript written on rapport_m2.log.
INFO - This is Biber 2.12
INFO - Logfile is 'rapport_m2.blg'
INFO - Reading 'rapport_m2.bcf'
INFO - Found 23 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'rapport_m2.bib' for section 0
INFO - LaTeX decoding ...
FATAL - Caught signal: SEGV
Likely your .bib has a very bad entry which causes libbtparse to crash: Inappropriate ioctl for device
./compil_rapport: line 14: 24506 Segmentation fault      biber rapport_m2

It seems coming from an issue from comma into my references "@article" : But why don't I have problems on MacOS and this issue on Debian/Linux, it's weird ...

UPDATE 2: I have more informations about my issue by doing :

$ biber --tool --debug debug_bib.tex
INFO - This is Biber 2.12 running in TOOL mode
INFO - Logfile is 'debug_bib.tex.blg'
INFO - DEBUG mode: all messages are logged to 'debug_bib.tex.blg'
INFO - Looking for bibtex format file 'debug_bib.tex'
Use of uninitialized value $benc in string eq at /usr/share/perl5/Biber/Input/file/bibtex.pm line 1465.
INFO - LaTeX decoding ...
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 11, warning: 63 characters of junk seen at toplevel
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 418, warning: 2105 characters of junk seen at toplevel
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 418, warning: "}" in strange place -- should get a syntax error
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 418, syntax error: found "}", expected one of: start of entry ("{" or "(") or quoted string ({...} or "...")
invalid token near line 419 (text was '\')
invalid token near line 419 (text was '\')
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 470, warning: 5 characters of junk seen at toplevel
Use of uninitialized value in concatenation (.) or string at /usr/share/perl5/Biber/Input/file/bibtex.pm line 1516.
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 470, syntax error: found "#", expected one of: start of entry ("{" or "(") or quoted string ({...} or "...")
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 550, warning: 907 characters of junk seen at toplevel
Use of uninitialized value in concatenation (.) or string at /usr/share/perl5/Biber/Input/file/bibtex.pm line 1516.
invalid token near line 550 (text was '\')
/tmp/Dh8o_Onbpd/debug_bib.tex_27990.utf8, line 550, syntax error: found "ppendix", expected one of: start of entry ("{" or "(") or quoted string ({...} or "...")
invalid token near line 551 (text was '\')
invalid token near line 552 (text was '\')
invalid token near line 553 (text was '\')
Use of uninitialized value in concatenation (.) or string at /usr/share/perl5/Biber/Input/file/bibtex.pm line 1516.
warning: overriding existing definition of macro "feb"
warning: overriding existing definition of macro "may"
warning: overriding existing definition of macro "nov"
warning: overriding existing definition of macro "mar"
warning: overriding existing definition of macro "oct"
warning: overriding existing definition of macro "aug"
warning: overriding existing definition of macro "jul"
warning: overriding existing definition of macro "apr"
warning: overriding existing definition of macro "jun"
warning: overriding existing definition of macro "jan"
warning: overriding existing definition of macro "dec"
warning: overriding existing definition of macro "sep"
FATAL - Caught signal: SEGV
Likely your .bib has a very bad entry which causes libbtparse to crash: Inappropriate ioctl for device

my file debug_bib.tex is located on this link : latex source for debuggging biber

UPDATE 3:

Here is the output of biber of MacOS version (where it compiles fine) :

warning: overriding existing definition of macro "mar"
warning: overriding existing definition of macro "jul"
warning: overriding existing definition of macro "feb"
warning: overriding existing definition of macro "sep"
warning: overriding existing definition of macro "nov"
warning: overriding existing definition of macro "may"
warning: overriding existing definition of macro "oct"
warning: overriding existing definition of macro "jun"
warning: overriding existing definition of macro "aug"
warning: overriding existing definition of macro "apr"
warning: overriding existing definition of macro "jan"
warning: overriding existing definition of macro "dec"
warning: comma(s) at end of name (removing)
author, warning: comma(s) at end of name (removing)
Use of uninitialized value $end in substitution (s///) at /opt/local/lib/perl5/vendor_perl/5.28/Biber/Input/file/bibtex.pm line 1023.
Use of uninitialized value $end in substitution (s///) at /opt/local/lib/perl5/vendor_perl/5.28/Biber/Input/file/bibtex.pm line 1023.
INFO - This is Biber 2.11
INFO - Logfile is 'rapport_m2.blg'
INFO - DEBUG mode: all messages are logged to 'rapport_m2.blg'
INFO - Reading 'rapport_m2.bcf'
INFO - Found 23 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'rapport_m2.bib' for section 0
INFO - LaTeX decoding ... 
INFO - Found BibTeX data source 'rapport_m2.bib'
INFO - Overriding locale 'fr-FR' defaults 'variable = shifted' with 'variable = non-ignorable'
INFO - Overriding locale 'fr-FR' defaults 'normalization = NFD' with 'normalization = prenormalized'
INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'fr-FR'
INFO - No sort tailoring available for locale 'fr-FR'
INFO - Writing 'rapport_m2.bbl' with encoding 'latin1'
INFO - Output to rapport_m2.bbl

with the .blg file asscoiated :

MacOS blg file output biber

and the .blg of Debian :

Debian blg file output biber

It would be interesting to compare them but it is difficult.

  • 1
    biber is not working on debian, you get perl errors: Can't locate autovivification.pm in @INC (you may need to install the autovivification module) – Ulrike Fischer Jun 20 at 15:32
  • @UlrikeFischer I have installed libautovivification-perl_0.18-1+b1_amd64.deb package which provides autovivification module and autovivification.pm file but issue remains. What is the alternative to biber on Debian/Linux ? – youpilat13 Jun 20 at 15:57
  • 1
    you need biber with biblatex. I'm on windows and can't help you to debug a debian problem. – Ulrike Fischer Jun 20 at 15:59
  • @UlrikeFischer However, I have declared as you can see above : \usepackage[style=ext-authoryear, backend=biber]{biblatex}, does it come from this ? – youpilat13 Jun 20 at 16:02
  • put \listfiles as first line into your document and compare the two file lists which itself can be found at the end of the log files. – user187802 Jun 20 at 16:08

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