[Debichem-devel] Bug#1112634: openms FTBFS: error from pdflatex
Helmut Grohne
helmut at subdivi.de
Fri Aug 29 15:54:21 BST 2025
Source: openms
Version: 2.6.0+cleaned1-4
Severity: serious
Tags: ftbfs
openms fails to build from source in unstable on amd64. This likely is a
very recent regression induced by one of its dependencies as it hasn't
been uploaded lately and neither https://crossqa.debian.net nor
reproducible builds noticed the failure yet. For some reason pdflatex
ends up failing. This also raises the question: Would it be possible to
skip the pdflatex stuff in arch-only builds? There is
-DBUILD_DOCS=ON/OFF and it defaults to ON, but since the documentation
is installed to an Arch:all package, we might skip doing it for each
architecture. Please find a build log below.
Helmut
| [ 94%] Build the OpenMS/TOPP pdf tutorial
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E echo ""
|
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E echo "Creating OpenMS pdf tutorial"
| Creating OpenMS pdf tutorial
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E echo ""
|
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E remove_directory OpenMS_tutorial/latex_output
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E chdir OpenMS_tutorial/ /usr/bin/doxygen Doxyfile
| warning: Tag 'TCL_SUBST' at line 247 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 'COLS_IN_ALPHA_INDEX' at line 1046 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_TIMESTAMP' at line 1182 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 'FORMULA_TRANSPARENT' at line 1463 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 'LATEX_SOURCE_CODE' at line 1751 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 'LATEX_TIMESTAMP' at line 1767 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 'RTF_SOURCE_CODE' at line 1833 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 'DOCBOOK_PROGRAMLISTING' at line 1931 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 'PERL_PATH' at line 2111 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 'CLASS_DIAGRAMS' at line 2124 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 'MSCGEN_PATH' at line 2133 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 'DOT_FONTNAME' at line 2175 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 'DOT_FONTSIZE' at line 2182 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 'DOT_TRANSPARENT' at line 2406 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: argument 'a4wide' for option PAPER_TYPE is not a valid enum value
| Using the default: a4!
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E copy OpenMS_tutorial/refman_overwrite.tex OpenMS_tutorial/latex_output/refman.tex
| cd /build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/doc && /usr/bin/cmake -E chdir OpenMS_tutorial/latex_output/ /usr/bin/pdflatex refman.tex
| This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex)
| restricted \write18 enabled.
| entering extended mode
| (./refman.tex
| LaTeX2e <2025-06-01> patch level 1
| L3 programming layer <2025-07-19>
| (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
| Document Class: article 2025/01/22 v1.4n Standard LaTeX document class
| (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
| (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
| (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.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/graphics.sty
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
| (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
| (/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/alltt.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/newtxtext.sty
| `newtxtext' v1.744, 2024/04/01 Text macros taking advantage of TeXGyre Termes a
| nd its extensions (msharpe)
| (/usr/share/texlive/texmf-dist/tex/latex/xpatch/xpatch.sty
| (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3.sty
| (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def))
| (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
| (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))
| (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
| (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
| (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex)))
| (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty
| (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex))
| (/usr/share/texlive/texmf-dist/tex/latex/carlisle/scalefnt.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/kastrup/binhex.tex)
| (/usr/share/texlive/texmf-dist/tex/latex/fontaxes/fontaxes.sty
| (/usr/share/texlive/texmf-dist/tex/latex/figureversions/figureversions.sty)))
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/newtxmath.sty
| `newtxmath' v1.754, 2024/09/22 Math macros based originally on txfonts (msharpe
| ) (/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/oberdiek/centernot.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/kastrup/binhex.tex)
| amsthm NOT loaded
| ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty
| (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
| (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)))
| (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
| (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
| (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
| (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
| (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/backref.sty
| (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
| (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
| (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))))
| (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def) (./doxygen.sty
| (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty
| (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
| (./longtable_doxygen.sty) (./tabu_doxygen.sty
| (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
| ==> First Aid for varwidth.sty applied!
| ) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hanging/hanging.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifpdf.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjustbox.sty
| (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjcalc.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/trimclip.sty
| (/usr/share/texlive/texmf-dist/tex/latex/collectbox/collectbox.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/tc-pdftex.def))
| (/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
| (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/stackengine/stackengine.sty
| (/usr/share/texlive/texmf-dist/tex/generic/listofitems/listofitems.sty
| (/usr/share/texlive/texmf-dist/tex/generic/listofitems/listofitems.tex)))
| (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/alphalph/alphalph.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty))
| Writing index file refman.idx
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/ot1ntxtlf.fd)
| No file refman.aux.
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/omlntxmi.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/untxexa.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/lmsntxsy.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/lmxntxexx.fd)
| *geometry* driver: auto-detecting
| *geometry* detected driver: pdftex
| (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
| [Loading MPS to PDF converter (version 2006.09.02).]
| ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
| [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-
| dist/fonts/enc/dvips/newtx/ntx-ot1-tlf.enc}]
| No file refman.toc.
|
|
| pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has
| been already used, duplicate ignored
| <to be read again>
| \relax
| l.64
| [1] (./tutorial.tex
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/ot1minntx.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/untxmia.fd)
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| Underfull \hbox (badness 10000) in paragraph at lines 5--6
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| (/usr/share/texlive/texmf-dist/tex/latex/newtx/ot1ntxtt.fd)
| Overfull \hbox (10.368pt too wide) in paragraph at lines 8--9
| \OT1/ntxtlf/m/n/10 so-phis-ti-cated al-go-rithms for data anal-y-sis ([][] \OT1
| /ntxtt/m/n/10 https[]://www.[]nature.[]com/nmeth/journal/v13/n9/abs/nmeth.[]
|
| Underfull \hbox (badness 10000) in paragraph at lines 8--9
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| [2]
| Underfull \hbox (badness 10000) in paragraph at lines 34--35
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| Underfull \hbox (badness 10000) in paragraph at lines 51--55
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| [3{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} <./OpenMS_overview.png
| (PNG copy)>]
| Underfull \hbox (badness 10000) in paragraph at lines 57--59
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| Underfull \hbox (badness 10000) in paragraph at lines 61--81
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| [4]
| Underfull \hbox (badness 10000) in paragraph at lines 101--102
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| Underfull \hbox (badness 10000) in paragraph at lines 103--104
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| [5 <./Terms_Spectrum.png>]
| Underfull \hbox (badness 10000) in paragraph at lines 116--118
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| [6 <./Terms_Map.png>]
| Overfull \hbox (5.6113pt too wide) in paragraph at lines 154--155
| []\OT1/ntxtlf/m/n/10 Untargeted, label-free (Tools Feature[]Finder[]Centroided,
| Feature[]Finder[]Multiplex, and its classes)
|
| Underfull \hbox (badness 10000) in paragraph at lines 184--185
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| Underfull \hbox (badness 10000) in paragraph at lines 233--234
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| [7]
| Underfull \hbox (badness 10000) in paragraph at lines 244--245
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| ! Extra }, or forgotten \endgroup.
| <recently read> \egroup
|
| l.263 \end{longtabu}
|
| ?
| ! Emergency stop.
| <recently read> \egroup
|
| l.263 \end{longtabu}
|
| ! ==> Fatal error occurred, no output PDF file produced!
| Transcript written on refman.log.
| make[4]: *** [doc/CMakeFiles/doc_tutorials.dir/build.make:81: doc/CMakeFiles/doc_tutorials] Error 1
| make[4]: Leaving directory '/build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu'
| make[3]: *** [CMakeFiles/Makefile2:9315: doc/CMakeFiles/doc_tutorials.dir/all] Error 2
| make[3]: Leaving directory '/build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu'
| make[2]: *** [Makefile:149: all] Error 2
| make[2]: Leaving directory '/build/reproducible-path/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu'
| dh_auto_install: error: cd obj-x86_64-linux-gnu && make -j1 install DESTDIR=/build/reproducible-path/openms-2.6.0\+cleaned1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" returned exit code 2
| make[1]: *** [debian/rules:140: override_dh_auto_install] Error 25
| make[1]: Leaving directory '/build/reproducible-path/openms-2.6.0+cleaned1'
| make: *** [debian/rules:43: binary] Error 2
| dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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