Bug#796832: pandoc generating bibliography issue

[Riccardo Romoli]

Package: pandoc
Version: 1.12.4.2

I would try to convert the way I write my scientific articles from 
Sweave/LaTeX to knitr/pandoc.
I've been able to reproduce almost everithing with the exceptions of the 
references.
I googled a lot and I read the official and unofficial guide to the 
pandoc references but I've not
yet found the right solution to my problem: no citations are included in 
my document.

This is what I've done:

     added bibliography: myBib.bib to the header of the file
     added the citation using [@KEY], where KEY is the key entry in my 
.bib file
     added # References section at the bottom of my document
     convert .Rmd file to .md file using knitr

     from shell I run:

     pandoc -H headers.tex --bibliography=myBib.bib -o article.pdf 
article.md

The .pdf file was generated but with non citation references

I've also tried to generate the .tex file and then to compile it

pandoc --bibliography=myBib.bib -o article.tex article.md

also using the --natbib and --biblatex switch, but nothing changes.
Opening the .tex file I noticed that the citations were converted as: 
{[}@01, @46{]}
while in the .md file I wrote: [@01, @46].

I installed pandoc (1.15.0.6) and pandoc-citeproc from source and all 
seems to work properly.


-- System Information:
Debian Release: 8.1
   APT prefers stable-updates
   APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.16.0-4-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages pandoc depends on:
ii  libc6        2.19-18
ii  libffi6      3.1-2+b2
ii  libgmp10     2:6.0.0+dfsg-6
ii  libicu52     52.1-8+deb8u2
ii  liblua5.1-0  5.1.5-7.1
ii  libpcre3     2:8.35-3.3
ii  libyaml-0-2  0.1.6-3
ii  pandoc-data  1.12.4.2~dfsg-1
ii  zlib1g       1:1.2.8.dfsg-2+b1

pandoc recommends no packages.

Versions of packages pandoc suggests:
pn  etoolbox                   <none>
ii  pandoc-citeproc            0.4.0.1-1
ii  texlive-latex-recommended  2014.20141024-2
ii  texlive-luatex             2014.20141024-2
ii  texlive-xetex              2014.20141024-2

-- no debconf information
-------------- next part --------------
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MIME-Version: 1.0
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From: Riccardo <ric.romoli at gmail.com>
To: Debian Bug Tracking System <700329 at bugs.debian.org>
Subject: pandoc generating bibliography issue
Message-ID: <20150824175846.29380.79392.reportbug at mb>
X-Mailer: reportbug 6.6.3
Date: Mon, 24 Aug 2015 19:58:46 +0200
X-Debbugs-Cc: ric.romoli at gmail.com

Package: pandoc
Followup-For: Bug #700329

Dear Maintainer,

*** Reporter, please consider answering these questions, where appropriate ***

   * What led up to the situation?
   * What exactly did you do (or not do) that was effective (or
     ineffective)?
   * What was the outcome of this action?
   * What outcome did you expect instead?


I would try to convert the way I write my scientific articles from Sweave/LaTeX to knitr/pandoc. 
I've been able to reproduce almost everithing with the exceptions of the references. 
I googled a lot and I read the official and unofficial guide to the pandoc references but I've not 
yet found the right solution to my problem: no citations are included in my document.

This is what I've done:

    added bibliography: myBib.bib to the header of the file
    added the citation using [@KEY], where KEY is the key entry in my .bib file
    added # References section at the bottom of my document
    convert .Rmd file to .md file using knitr

    from shell I run:

    pandoc -H headers.tex --bibliography=myBib.bib -o article.pdf article.md

The .pdf file was generated but with non citation references

I've also tried to generate the .tex file and then to compile it 

pandoc --bibliography=myBib.bib -o article.tex article.md 

also using the --natbib and --biblatex switch, but nothing changes. 
Opening the .tex file I noticed that the citations were converted as: {[}@01, @46{]} 
while in the .md file I wrote: [@01, @46].

I installed pandoc and pandoc-citeproc from source and all seems to work properly.



*** End of the template - remove these template lines ***


-- System Information:
Debian Release: 8.1
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.16.0-4-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages pandoc depends on:
ii  libc6        2.19-18
ii  libffi6      3.1-2+b2
ii  libgmp10     2:6.0.0+dfsg-6
ii  libicu52     52.1-8+deb8u2
ii  liblua5.1-0  5.1.5-7.1
ii  libpcre3     2:8.35-3.3
ii  libyaml-0-2  0.1.6-3
ii  pandoc-data  1.12.4.2~dfsg-1
ii  zlib1g       1:1.2.8.dfsg-2+b1

pandoc recommends no packages.

Versions of packages pandoc suggests:
pn  etoolbox                   <none>
ii  pandoc-citeproc            0.4.0.1-1
ii  texlive-latex-recommended  2014.20141024-2
ii  texlive-luatex             2014.20141024-2
ii  texlive-xetex              2014.20141024-2

-- no debconf information