[Debichem-devel] Bug#963637: rdkit: FTBFS with Sphinx 3.1: ! LaTeX Error: Too deeply nested.
Lucas Nussbaum
lucas at debian.org
Wed Jun 24 21:52:40 BST 2020
Source: rdkit
Version: 201909.1-4.1
Severity: important
Tags: ftbfs
User: python-modules-team at lists.alioth.debian.org
Usertags: sphinx3.1
Hi,
rdkit fails to build with Sphinx 3.1, currently available in
experimental.
Relevant part (hopefully):
> make[3]: Entering directory '/<<PKGBUILDDIR>>/Docs/Book/_build/latex'
> latexmk -pdf -dvi- -ps- 'RDKit.tex'
> Rc files read:
> /etc/LatexMk
> latexmkrc
> Latexmk: This is Latexmk, John Collins, 17 Apr. 2020, version: 4.69a.
> Rule 'pdflatex': The following rules & subrules became out-of-date:
> 'pdflatex'
> ------------
> Run number 1 of rule 'pdflatex'
> ------------
> ------------
> Running 'pdflatex -recorder "RDKit.tex"'
> ------------
> Latexmk: applying rule 'pdflatex'...
> This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
> restricted \write18 enabled.
> entering extended mode
> (./RDKit.tex
> LaTeX2e <2020-02-02> patch level 5
> L3 programming layer <2020-05-15> (./sphinxmanual.cls
> Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
> (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
> Document Class: report 2019/12/20 v1.4l Standard LaTeX document class
> (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
> (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<<t1.cmap>>)
> (/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/amssymb.sty
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
> (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
> (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
> (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))
> (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
> (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.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/graphics-cfg/graphics.cfg)
> (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
> (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
> (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
> (./sphinxmulticell.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.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/fancyvrb/fancyvrb.sty)
> (./footnotehyper-sphinx.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty
> (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip-2001-04-09.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
> (./sphinxhighlight.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
> (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)))
> (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.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/hyperref/hyperref.sty
> (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
> (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.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/latex/hycolor/hycolor.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.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/generic/etexcmds/etexcmds.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
> (/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/generic/bigintcalc/bigintcalc.sty))
> (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
> (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.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/latex/oberdiek/hypcap.sty)
> (./sphinxmessages.sty)
> Writing index file RDKit.idx
> (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
> (./RDKit.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
> (/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))
> *geometry* driver: auto-detecting
> *geometry* detected driver: pdftex
> (/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/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
> >><<oms.cmap>><<omx.cmap>>
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
> nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2]
> (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
> Underfull \hbox (badness 10000) in paragraph at lines 174--175
> []\T1/ptm/m/n/10 [stk]([][]$https : / / github . com / lukasturcani / stk$[][])
> ([docs]([][]$https : / / lukasturcani . github . io / stk / docs / build / htm
> l/$[][]), [pa-
> [1] [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
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> Underfull \hbox (badness 10000) in paragraph at lines 287--288
> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 bash Miniconda3-latest-MacOSX-x86_64.sh con
> da install numpy matplotlib conda
>
> Underfull \hbox (badness 10000) in paragraph at lines 287--288
> \T1/pcr/m/n/10 install cmake cairo pillow eigen pkg-config conda install boost-
> cpp boost
>
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> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 RDBASE=$RDBASE DYLD_FALLBACK_LIBRARY_PATH="
> $RDBASE/lib:$PYROOT/lib"
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> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 bash Anaconda3-5.2.0-x86_64.sh conda instal
> l -y cmake cairo pillow eigen
> [3]
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> []\T1/ptm/m/n/10 -DRDK_INSTALL_INTREE=ON -DRDK_INSTALL_STATIC_LIBS=OFF -
>
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> \T1/ptm/m/n/10 DRDK_BUILD_CPP_TESTS=ON -DPYTHON_NUMPY_INCLUDE_PATH=^^Q$(python
> -c `im-port
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> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 [conda folder]/envs/my-rdkit-env/bin/initdb
> -D /folder/where/data/should/be/
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> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 cmake -D PYTHON_LIBRARY=/usr/lib/python3.6/
> config/libpython3.6.a -D
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> []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the
> ar-gu-ment \T1/ptm/m/it/10 -
> [6]
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> ython 2.2.1 on
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> \T1/pcr/m/n/10 java1.6.0_20 Type "copyright", "credits" or "license" for more i
> nformation.
>
> Underfull \hbox (badness 10000) in paragraph at lines 616--617
> \T1/pcr/m/n/10 >>> from org.RDKit import * >>> from java import lang >>> lang.S
> ystem.
>
> Underfull \hbox (badness 10000) in paragraph at lines 616--617
> \T1/pcr/m/n/10 loadLibrary(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 GraphMolWrap\TS1/pcr
> /m/n/10 '\T1/pcr/m/n/10 ) >>> m = RWMol.MolFromSmiles(\TS1/pcr/m/n/10 '\T1/pcr/
> m/n/10 c1ccccc1\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ) >>> m.
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
> (textcomp) font family pcr in TS1 encoding.
> (textcomp) Default family used instead on input line 1.
>
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
> (textcomp) font family pcr in TS1 encoding.
> (textcomp) Default family used instead on input line 1.
>
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
> (textcomp) font family pcr in TS1 encoding.
> (textcomp) Default family used instead on input line 1.
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 Linking CXX shared library libSLNParse.so /
> usr/bin/ld: .../
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> \T1/pcr/m/n/10 libboost_regex.a(cpp_regex_traits.o): relocation R_X86_64_32S ag
> ainst
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> \TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 std::basic_string<char, std::char_traits<char>
> , std::allocator<char>
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> \T1/pcr/m/n/10 >::_Rep::_S_empty_rep_storage\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ca
> n not be used when making a shared object;
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> \T1/pcr/m/n/10 recompile with -fPIC .../libboost_regex.a: could not read symbol
> s: Bad value
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> \T1/pcr/m/n/10 collect2: ld returned 1 exit status make[2]: *** [Code/GraphMol/
> SLNParse/
>
> Underfull \hbox (badness 10000) in paragraph at lines 637--638
> \T1/pcr/m/n/10 libSLNParse.so] Error 1 make[1]: *** [Code/GraphMol/SLNParse/CMa
> keFiles/
>
> ! LaTeX Error: Too deeply nested.
>
> See the LaTeX manual or LaTeX Companion for explanation.
> Type H <return> for immediate help.
> ...
>
> l.648 \item {} \begin{itemize}
>
> ?
> ! Emergency stop.
> ...
>
> l.648 \item {} \begin{itemize}
>
> ! ==> Fatal error occurred, no output PDF file produced!
> Transcript written on RDKit.log.
> Latexmk: Index file 'RDKit.idx' was written
> Collected error summary (may duplicate other messages):
> pdflatex: Command for 'pdflatex' gave return code 1
> Refer to 'RDKit.log' for details
> Latexmk: Use the -f option to force complete processing,
> unless error was exceeding maximum runs, or warnings treated as errors.
> === TeX engine is 'pdfTeX'
> Latexmk: Errors, so I did not complete making targets
> make[3]: *** [Makefile:29: RDKit.pdf] Error 12
The full build log is available from:
http://qa-logs.debian.net/2020/06/23/rdkit_201909.1-4.1_unstable_sphinx-exp.log
Please see [1] for Sphinx changelog, which may give a hint of what changes in
Sphinx caused this error.
Also see [2] for the list of deprecated/removed APIs and possible alternatives
to them.
Sphinx 3.1 is going to be uploaded to unstable in a couple of weeks. When that
happens, the severity of this bug will be bumped to serious.
In case you have questions, please Cc sphinx at packages.debian.org on reply.
[1]: https://www.sphinx-doc.org/en/3.x/changes.html
[2]: https://www.sphinx-doc.org/en/3.x/extdev/deprecated.html
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.
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