Your message dated Sat, 10 Jan 2026 15:24:44 +0100
with message-id <[email protected]>
and subject line Re: Bug#1112634: doxygen is not compatible with the latest TeX
Live
has caused the Debian Bug report #1112634,
regarding doxygen is not compatible with the latest TeX Live
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
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--
1112634: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1112634
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/untxsym.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/untxsyc.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
| Underfull \hbox (badness 10000) in paragraph at lines 5--6
|
| (/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
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 11--12
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 14--15
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 17--18
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 20--21
|
|
| [2]
| Underfull \hbox (badness 10000) in paragraph at lines 34--35
|
| (/usr/share/texlive/texmf-dist/tex/latex/newtx/ts1ntxtlf.fd)
| Underfull \hbox (badness 10000) in paragraph at lines 39--40
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 41--42
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 43--44
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 45--46
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 51--55
|
|
| [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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| Underfull \hbox (badness 10000) in paragraph at lines 61--81
|
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| Underfull \hbox (badness 10000) in paragraph at lines 61--81
|
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| Underfull \hbox (badness 10000) in paragraph at lines 61--81
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| Underfull \hbox (badness 10000) in paragraph at lines 61--81
|
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| Underfull \hbox (badness 10000) in paragraph at lines 84--85
|
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| Underfull \hbox (badness 10000) in paragraph at lines 86--87
|
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| Underfull \hbox (badness 10000) in paragraph at lines 88--89
|
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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
|
|
| [5 <./Terms_Spectrum.png>]
| Underfull \hbox (badness 10000) in paragraph at lines 116--118
|
|
| [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
|
|
| Underfull \hbox (badness 10000) in paragraph at lines 233--234
|
|
| [7]
| Underfull \hbox (badness 10000) in paragraph at lines 244--245
|
| ! 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
--- End Message ---
--- Begin Message ---
Version: 1.15.0+ds1-1
Am 09.01.2026 um 00:09 schrieb Santiago Vila:
Hello. I still can't build three of the packages in the affects for this bug:
bliss
libest
log4c
I've opened Bug#1125194 & Bug#1125179 and am closing this issue again.
Hilmar
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--- End Message ---
