search

MDAnalysis / scipy_proceedings

SciPy conference proceedings: MDAnalysis paper
Other
0 stars 4 forks source link

can't build paper #4

Closed kain88-de closed 8 years ago

kain88-de commented 8 years ago 
./make_paper.sh papers/oliver_beckstein
Building: oliver_beckstein
PDFLaTeX error output:
================================================================================
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./paper.tex
LaTeX2e <2011/06/27>
Babel <3.9k> and hyphenation patterns for 75 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/IEEEtran/IEEEtran.cls
Document Class: IEEEtran 2012/12/27 V1.8 by Michael Shell
-- See the "IEEEtran_HOWTO" manual for usage information.
-- http://www.michaelshell.org/tex/ieeetran/
-- Using IEEE Computer Society mode.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ppl.fd)
-- Using 8.5in x 11in (letter) paper.
-- Using PDF output.
-- This is a 10 point document.
) (/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty)
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ppl.fd)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (./scipy.sty
(./status.sty
(/usr/share/texlive/texmf-dist/tex/latex/draftwatermark/draftwatermark.sty
(/usr/share/texlive/texmf-dist/tex/latex/everypage/everypage.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/helvet.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/courier.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `pdftex' has already been used,
(hyperref)                setting the option has no effect on input line 39.

(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./paper.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./paper.out) (./paper.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)<<ot1.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)<<oml.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)<<oms.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd)<<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/upzd.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Underfull \hbox (badness 2941) in paragraph at lines 206--207
\T1/ptm/m/n/10 Gen-eral Pub-lic Li-cense v2 from GitHub [][]$https : / / github
 .
[1{/usr/share/texlive/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}]
(./paper.bbl
Underfull \hbox (badness 10000) in paragraph at lines 5--10
[]\T1/ptm/m/n/8 Naveen Michaud-Agrawal, Eliz-a-beth Jane Den-ning,

Underfull \hbox (badness 2142) in paragraph at lines 12--16
\T1/ptm/m/n/8 ti-fy-ing macro-molec-u-lar path-ways.  \T1/ptm/m/it/8 PLoS Com-p
ut Biol\T1/ptm/m/n/8 ,

Underfull \hbox (badness 3271) in paragraph at lines 23--27
[]\T1/ptm/m/n/8 Matteo Tib-erti, Elena Pa-pa-leo, Tone Bengt-sen, Wouter
) [2
! pdfTeX error (ext4): \pdfendlink ended up in different nesting level than \pd
fstartlink.
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.223 \end{document}

!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on paper.log.

================================================================================

I've installed the texlive packages they list as well as the python packages. But this looks to me like some tex conversion error.

orbeckst commented 8 years ago

I can only contribute the unhelpful "works for me" (on Mac OS 10.11.5 with texlive in macports). I am attaching my paper.log.txt for comparison.

Did you try "divide and conquer", i.e., chopping out halves of the paper and seeing if the error persists?

It could also be a problem with how links from the bibliography are broken across lines.

richardjgowers commented 8 years ago

Looks like it's caused by hyperref, does removing this make it compile?

kain88-de commented 8 years ago

I can't remove hyperref. But playing with the ReST file I notice that everything compiles once I remove the bibliography. So it looks like that needs to be updated.

kain88-de commented 8 years ago

ok wrong alarm with the bibliography. Line93 with all the github links causes problems.

kain88-de commented 8 years ago

Ok I figured it out. My latex version only doesn't like constructs like \url{https://some.url.org/extra. If the url ends in something like .org or similar it works.

kain88-de commented 8 years ago

Aha Know I found the error. This is a very tricky one. Basically the linebreak occurs on line 93 for the link to our github repo. Apparently hyperref doesn't like line breaks. OMFG why does this compile for Oliver then -,-

http://tex.stackexchange.com/questions/1522/pdfendlink-ended-up-in-different-nesting-level-than-pdfstartlink#154184

kain88-de commented 8 years ago

I'll just accept then that my current latex installation is broken with hyperref for some reason.

richardjgowers commented 8 years ago

I get this too on one of my computers, seems like a common error and most the fixes I find we can't use because the .tex is invisible to us mostly

kain88-de commented 8 years ago

Not invisible but we can't do much about the construction of it. The only thing that would help is using shorter links. But that is not good for people who print the proceedings (a colleague actually does this!)