Your message dated Wed, 23 Sep 2020 07:49:55 +0000
with message-id <e1kkzxh-000ea7...@fasolo.debian.org>
and subject line Bug#963637: fixed in rdkit 202003.4-2
has caused the Debian Bug report #963637,
regarding rdkit: FTBFS with Sphinx 3.1: ! LaTeX Error: Too deeply nested.
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
Bug report if necessary, and/or fix the problem forthwith.
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--
963637: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963637
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: rdkit
Version: 201909.1-4.1
Severity: important
Tags: ftbfs
User: python-modules-t...@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 Rule 'pdflatex': The following rules & subrules became out-of-date: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)
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
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> (textcomp) Default family used instead on input line 239.
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> (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.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
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
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> Underfull \hbox (badness 10000) in paragraph at lines 304--305
> []\T1/ptm/m/n/10 -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_CAIRO_SUPPORT=ON -
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
> (textcomp) font family ptm in TS1 encoding.
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> Underfull \hbox (badness 10000) in paragraph at lines 313--314
> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 RDBASE=$RDBASE
> DYLD_FALLBACK_LIBRARY_PATH="
> $RDBASE/lib:$PYROOT/lib"
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
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> Underfull \hbox (badness 10000) in paragraph at lines 328--329
> []\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]
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
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> Underfull \hbox (badness 10000) in paragraph at lines 345--346
> []\T1/ptm/m/n/10 -DRDK_INSTALL_INTREE=ON -DRDK_INSTALL_STATIC_LIBS=OFF -
>
> Underfull \hbox (badness 5504) in paragraph at lines 345--346
> \T1/ptm/m/n/10 DRDK_BUILD_CPP_TESTS=ON
> -DPYTHON_NUMPY_INCLUDE_PATH=^^Q$(python
> -c `im-port
>
> Package textcomp Warning: Symbol \textasciigrave not provided by
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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 [conda
> folder]/envs/my-rdkit-env/bin/postgr
> es -D /folder/where/data/should/
>
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> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 [program:postgresql] command=[conda
> folder]
> /envs/my-rdkit-env/bin/postgres
>
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> []\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 shellsession $ wget
> https://github.com/rdkit
> /rdkit/archive/Release_XXXX_XX_X.
> [5]
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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
>
> Underfull \hbox (badness 10000) in paragraph at lines 555--556
> \T1/pcr/m/n/10 PYTHON_INCLUDE_DIR=/usr/include/python3.6/ -D
> PYTHON_EXECUTABLE=
> /usr/bin/
>
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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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>
>
> Underfull \hbox (badness 10000) in paragraph at lines 616--617
> []\TS1/cmtt/m/n/10 ` \T1/pcr/m/n/10 $
> CLASSPATH=$CLASSPATH:$RDBASE/Code/JavaWra
> ppers/gmwrapper/org.RDKit.jar
>
> Underfull \hbox (badness 10000) in paragraph at lines 616--617
> \T1/pcr/m/n/10 jython -Djava.library.path=$RDBASE/Code/JavaWrappers/gmwrapper
> J
> ython 2.2.1 on
>
> Underfull \hbox (badness 10000) in paragraph at lines 616--617
> \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 sph...@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.
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202003.4-2
Done: Michael Banck <mba...@debian.org>
We believe that the bug you reported is fixed in the latest version of
rdkit, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 963...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael Banck <mba...@debian.org> (supplier of updated rdkit package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 23 Sep 2020 09:35:31 +0200
Source: rdkit
Architecture: source
Version: 202003.4-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Michael Banck <mba...@debian.org>
Closes: 963637 964656
Changes:
rdkit (202003.4-2) unstable; urgency=medium
.
* debian/patches/postgres_compile_fixes.patch: New patch, fixes compile
errors on PostgreSQL-12 (Closes: #964656).
* debian/patches/sphinx_compile_fixes.patch: New patch, fixes build failures
with Sphinx-3.1 (Closes: #963637).
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