[Debichem-devel] Bug#753216: openms: FTBFS: Latex errors

[David Suárez]

Source: openms
Version: 1.11.1-3
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20140628 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[4]: Entering directory '/«PKGBUILDDIR»/debian/build'
> /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/debian/build/CMakeFiles 
> Build the OpenMS/TOPP pdf tutorial
> /usr/bin/cmake -E echo ""
> 
> /usr/bin/cmake -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /usr/bin/cmake -E echo "Creating OpenMS pdf tutorial"
> Creating OpenMS pdf tutorial
> /usr/bin/cmake -E echo ""
> 
> /usr/bin/cmake -E remove_directory doc/OpenMS_tutorial/latex_output
> /usr/bin/cmake -E chdir doc/OpenMS_tutorial/ doxygen Doxyfile
> Warning: Tag `DETAILS_AT_TOP' at line 43 of file `Doxyfile' has become obsolete.
>          To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> Warning: Tag `SHOW_DIRECTORIES' at line 80 of file `Doxyfile' has become obsolete.
>          To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> Warning: Tag `HTML_ALIGN_MEMBERS' at line 132 of file `Doxyfile' has become obsolete.
>          To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> Warning: Tag `XML_SCHEMA' at line 179 of file `Doxyfile' has become obsolete.
>          To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> Warning: Tag `XML_DTD' at line 180 of file `Doxyfile' has become obsolete.
>          To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> /usr/bin/cmake -E copy doc/OpenMS_tutorial/refman_overwrite.tex doc/OpenMS_tutorial/latex_output/refman.tex
> /usr/bin/cmake -E chdir doc/OpenMS_tutorial/latex_output/ pdflatex refman.tex
> This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014/Debian) (preloaded format=pdflatex)
>  restricted \write18 enabled.
> entering extended mode
> (./refman.tex
> LaTeX2e <2014/05/01>
> Babel <3.9k> and hyphenation patterns for 2 languages loaded.
> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
> Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
> (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
> (/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
> (/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.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/tools/multicol.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
> (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.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/hyperref/backref.sty
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
> 
> Package hyperref Message: Driver: hpdftex.
> 
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def) (./doxygen.sty
> (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
> (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
> (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/xtab/xtab.sty))
> Writing index file refman.idx
> No file refman.aux.
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.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))
> [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]pdfTeX warning (ext4): de
> stination with the same identifier (name{page.1}) has been already used, duplic
> ate ignored
> <to be read again> 
>                    \relax 
> l.43 
>       [1] (./tutorial_general.tex
> ! Undefined control sequence.
> l.1 ...utorial gives an introduction to the Open\+
>                                                   M\+S core datastructures a...
> 
> ? 
> ! Emergency stop.
> l.1 ...utorial gives an introduction to the Open\+
>                                                   M\+S core datastructures a...
> 
> !  ==> Fatal error occurred, no output PDF file produced!
> Transcript written on refman.log.
> make[4]: *** [CMakeFiles/doc_tutorials] Error 1

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2014/06/28/openms_1.11.1-3_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.