karthik / smb_git

A review paper describing how git can be used to improve reproducibility in science

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Pandoc problems

lsaravia opened this issue · comments

pandoc version is 1.9.1.1

This is the command you have en knit.sh

leonardo@lypMini:~/Dropbox/Pandoc$pandoc -H margins.sty --bibliography git_ms.bib --csl plos.csl git_manuscript.md -o git_manuscript.pdf

process_eprint: neprint=6 netype=-1
process_eprint: neprint=7 netype=-1

it displays these two lines and hangs. But when I try it without bibliography

leonardo@lypMini:~/Dropbox/Pandoc$ pandoc -H margins.sty git_manuscript.md -o git_manuscript.pdf

it works.

I tried also with another manuscript I am using as a test:

 leonardo@lypMini:~/Dropbox/Multifractals$ pandoc --template mytemplate.latex --bibliography /home/leonardo/BibTeX/library.bib mpnc.md -o mpnc.pdf 

 process_eprint: neprint=7 netype=-1
 Segmentation fault (core dumped)

But when I try without the bibliography another error appears,
because I copy&paste the text from Libre Office:

 pandoc --template mytemplate.latex "mpnc.md -o mpnc.pdf 
 pandoc: Error producing PDF from TeX source.
 ! Package inputenc Error: Unicode char \u8:⁠ not set up for use with LaTeX.

 See the inputenc package documentation for explanation.
 Type  H <return>  for immediate help.
 ...                                              

 l.72 Wagner and Fortin 2005)⁠

This error is because the Libre Office mendeley plugin inserted an invisible \u8 char after each citation. Anyway I have to delete every citation and put them in bib format, ok I deleted all citations and it works. At this point I try again with the bibliography and the same error appears.

  pandoc --template mytemplate.latex --bibliography /home/leonardo/BibTeX/library.bib  mnpc.md -o mpnc.pdf
  process_eprint: neprint=7 netype=-1
  Violación de segmento (`core' generado)

Everything solved installing the last pandoc version via cabal as described in http://johnmacfarlane.net/pandoc/installing.html

Except the problem with unicode char \u8 that I have to delete by hand (using sublime tex 2 was easy)

Great! There is also this to help with unicode characters: http://inundata.org/2012/12/04/how-to-ditch-word/#comment-487