[Debichem-devel] Bug#1042660: votca: FTBFS with Sphinx 7.1, docutils 0.20: make[5]: *** [share/doc/CMakeFiles/doc.dir/build.make:81: share/doc/CMakeFiles/doc] Error 2

[Lucas Nussbaum]

Source: votca
Version: 2022.1-1
Severity: important
Tags: ftbfs
User: python-modules-team at lists.alioth.debian.org
Usertags: sphinx7.1

Hi,

votca fails to build with Sphinx 7.1 and docutils 0.20, both of which
are currently available in experimental.

Relevant part (hopefully):
> make[5]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 98%] Generating ../../sphinx/customLogo.png
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/customLogo.png /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/customLogo.png
> [ 98%] Generating ../../sphinx/Architecture.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/Architecture.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/Architecture.rst
> [ 98%] Generating ../../sphinx/CODE_OF_CONDUCT.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/CODE_OF_CONDUCT.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/CODE_OF_CONDUCT.rst
> [ 98%] Generating ../../sphinx/DEVELOPERS_GUIDE.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/DEVELOPERS_GUIDE.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/DEVELOPERS_GUIDE.rst
> [ 98%] Generating ../../sphinx/INSTALL.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/INSTALL.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/INSTALL.rst
> [ 98%] Generating ../../sphinx/VOTCA_LANGUAGE_GUIDE.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/VOTCA_LANGUAGE_GUIDE.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/VOTCA_LANGUAGE_GUIDE.rst
> [100%] Generating ../../sphinx/index.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/index.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/index.rst
> [100%] Generating ../../sphinx/websiteAndDocumentation.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/cmake -E copy_if_different /<<PKGBUILDDIR>>/share/doc/websiteAndDocumentation.rst /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/websiteAndDocumentation.rst
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/share/doc && /usr/bin/sphinx-build /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx.html
> Running Sphinx v7.1.1
> making output directory... done
> building [mo]: targets for 0 po files that are out of date
> writing output... 
> building [html]: targets for 207 source files that are out of date
> updating environment: [new config] 207 added, 0 changed, 0 removed
> reading sources... [  0%] Architecture
> reading sources... [  1%] CODE_OF_CONDUCT
> reading sources... [  1%] DEVELOPERS_GUIDE
> reading sources... [  2%] INSTALL
> reading sources... [  2%] VOTCA_LANGUAGE_GUIDE
> reading sources... [  3%] csg-tutorials/README
> reading sources... [  3%] csg/advanced_topics
> reading sources... [  4%] csg/bibliography
> reading sources... [  4%] csg/csg_boltzmann
> reading sources... [  5%] csg/csg_call
> reading sources... [  5%] csg/csg_defaults
> reading sources... [  6%] csg/csg_density
> reading sources... [  6%] csg/csg_dlptopol
> reading sources... [  7%] csg/csg_dump
> reading sources... [  7%] csg/csg_fluctuations
> reading sources... [  8%] csg/csg_fmatch
> reading sources... [  8%] csg/csg_gmxtopol
> reading sources... [  9%] csg/csg_imc_solve
> reading sources... [  9%] csg/csg_inverse
> reading sources... [ 10%] csg/csg_map
> reading sources... [ 10%] csg/csg_orientcorr
> reading sources... [ 11%] csg/csg_part_dist
> reading sources... [ 11%] csg/csg_partial_rdf
> reading sources... [ 12%] csg/csg_property
> reading sources... [ 12%] csg/csg_radii
> reading sources... [ 13%] csg/csg_resample
> reading sources... [ 13%] csg/csg_reupdate
> reading sources... [ 14%] csg/csg_scripts
> reading sources... [ 14%] csg/csg_sphericalorder
> reading sources... [ 14%] csg/csg_stat
> reading sources... [ 15%] csg/csg_table
> reading sources... [ 15%] csg/csg_traj_force
> reading sources... [ 16%] csg/index
> reading sources... [ 16%] csg/input_files
> reading sources... [ 17%] csg/introduction
> reading sources... [ 17%] csg/mapping
> reading sources... [ 18%] csg/methods
> reading sources... [ 18%] csg/preparing
> reading sources... [ 19%] csg/reference
> reading sources... [ 19%] csg/scripts/add_POT.pl
> reading sources... [ 20%] csg/scripts/add_pot_generic.sh
> reading sources... [ 20%] csg/scripts/calc_density_generic.sh
> reading sources... [ 21%] csg/scripts/calc_kbint.sh
> reading sources... [ 21%] csg/scripts/calc_pressure_gromacs.sh
> reading sources... [ 22%] csg/scripts/calc_pressure_lammps.sh
> reading sources... [ 22%] csg/scripts/calc_rdf_generic.sh
> reading sources... [ 23%] csg/scripts/calc_target_rdf_generic.sh
> reading sources... [ 23%] csg/scripts/clean_generic.sh
> reading sources... [ 24%] csg/scripts/cma_processor.py
> reading sources... [ 24%] csg/scripts/convergence_check_default.sh
> reading sources... [ 25%] csg/scripts/dist_adjust.pl
> reading sources... [ 25%] csg/scripts/dist_boltzmann_invert.pl
> reading sources... [ 26%] csg/scripts/dummy.sh
> reading sources... [ 26%] csg/scripts/functions_common.sh
> reading sources... [ 27%] csg/scripts/functions_dlpoly.sh
> reading sources... [ 27%] csg/scripts/functions_genericsim.sh
> reading sources... [ 28%] csg/scripts/functions_gromacs.sh
> reading sources... [ 28%] csg/scripts/iie.py
> reading sources... [ 29%] csg/scripts/imc_stat_generic.sh
> reading sources... [ 29%] csg/scripts/initialize_step_generic.sh
> reading sources... [ 29%] csg/scripts/initialize_step_genericsim.sh
> reading sources... [ 30%] csg/scripts/initialize_step_optimizer.sh
> reading sources... [ 30%] csg/scripts/initialize_step_re.sh
> reading sources... [ 31%] csg/scripts/inverse.sh
> reading sources... [ 31%] csg/scripts/kbibi_ramp_correction.pl
> reading sources... [ 32%] csg/scripts/lj_126.pl
> reading sources... [ 32%] csg/scripts/merge_tables.pl
> reading sources... [ 33%] csg/scripts/optimizer_parameters_to_potential.sh
> reading sources... [ 33%] csg/scripts/optimizer_prepare_state.sh
> reading sources... [ 34%] csg/scripts/optimizer_state_to_mapping.sh
> reading sources... [ 34%] csg/scripts/optimizer_state_to_potentials.sh
> reading sources... [ 35%] csg/scripts/optimizer_target_density.sh
> reading sources... [ 35%] csg/scripts/optimizer_target_pressure.sh
> reading sources... [ 36%] csg/scripts/optimizer_target_rdf.sh
> reading sources... [ 36%] csg/scripts/post_add.sh
> reading sources... [ 37%] csg/scripts/post_add_single.sh
> reading sources... [ 37%] csg/scripts/post_update_generic.sh
> reading sources... [ 38%] csg/scripts/post_update_generic_single.sh
> reading sources... [ 38%] csg/scripts/post_update_re_single.sh
> reading sources... [ 39%] csg/scripts/postadd_acc_convergence.sh
> reading sources... [ 39%] csg/scripts/postadd_average.sh
> reading sources... [ 40%] csg/scripts/postadd_compress.sh
> reading sources... [ 40%] csg/scripts/postadd_convergence.sh
> reading sources... [ 41%] csg/scripts/postadd_copyback.sh
> reading sources... [ 41%] csg/scripts/postadd_dummy.sh
> reading sources... [ 42%] csg/scripts/postadd_overwrite.sh
> reading sources... [ 42%] csg/scripts/postadd_plot.sh
> reading sources... [ 43%] csg/scripts/postadd_shift.sh
> reading sources... [ 43%] csg/scripts/postadd_smooth_at_cut_off.sh
> reading sources... [ 43%] csg/scripts/postupd_addlj.sh
> reading sources... [ 44%] csg/scripts/postupd_cibi_correction.sh
> reading sources... [ 44%] csg/scripts/postupd_extrapolate.sh
> reading sources... [ 45%] csg/scripts/postupd_ibi.sh
> reading sources... [ 45%] csg/scripts/postupd_kbibi_correction.sh
> reading sources... [ 46%] csg/scripts/postupd_pressure.sh
> reading sources... [ 46%] csg/scripts/postupd_scale.sh
> reading sources... [ 47%] csg/scripts/postupd_smooth.sh
> reading sources... [ 47%] csg/scripts/postupd_splinesmooth.sh
> reading sources... [ 48%] csg/scripts/potential_extrapolate.sh
> reading sources... [ 48%] csg/scripts/potential_shift.pl
> reading sources... [ 49%] csg/scripts/potential_to_dlpoly.sh
> reading sources... [ 49%] csg/scripts/potential_to_generic.sh
> reading sources... [ 50%] csg/scripts/potential_to_gromacs.sh
> reading sources... [ 50%] csg/scripts/potential_to_lammps.sh
> reading sources... [ 51%] csg/scripts/potentials_to_dlpoly.sh
> reading sources... [ 51%] csg/scripts/potentials_to_generic.sh
> reading sources... [ 52%] csg/scripts/pre_update_re.sh
> reading sources... [ 52%] csg/scripts/prepare_generic.sh
> reading sources... [ 53%] csg/scripts/prepare_generic_single.sh
> reading sources... [ 53%] csg/scripts/prepare_iie.sh
> reading sources... [ 54%] csg/scripts/prepare_imc.sh
> reading sources... [ 54%] csg/scripts/prepare_optimizer.sh
> reading sources... [ 55%] csg/scripts/prepare_optimizer_single.sh
> reading sources... [ 55%] csg/scripts/prepare_re.sh
> reading sources... [ 56%] csg/scripts/pressure_cor_simple.pl
> reading sources... [ 56%] csg/scripts/pressure_cor_wjk.pl
> reading sources... [ 57%] csg/scripts/resample_target.sh
> reading sources... [ 57%] csg/scripts/run_genericsim.sh
> reading sources... [ 57%] csg/scripts/run_gromacs.sh
> reading sources... [ 58%] csg/scripts/simplex_downhill_processor.pl
> reading sources... [ 58%] csg/scripts/table_average.sh
> reading sources... [ 59%] csg/scripts/table_change_flag.sh
> reading sources... [ 59%] csg/scripts/table_combine.pl
> reading sources... [ 60%] csg/scripts/table_dummy.sh
> reading sources... [ 60%] csg/scripts/table_extrapolate.pl
> reading sources... [ 61%] csg/scripts/table_functional.sh
> reading sources... [ 61%] csg/scripts/table_get_value.pl
> reading sources... [ 62%] csg/scripts/table_integrate.pl
> reading sources... [ 62%] csg/scripts/table_linearop.pl
> reading sources... [ 63%] csg/scripts/table_scale.pl
> reading sources... [ 63%] csg/scripts/table_smooth.pl
> reading sources... [ 64%] csg/scripts/table_smooth_at_cut_off.py
> reading sources... [ 64%] csg/scripts/table_switch_border.pl
> reading sources... [ 65%] csg/scripts/table_to_tab.pl
> reading sources... [ 65%] csg/scripts/table_to_xvg.pl
> reading sources... [ 66%] csg/scripts/tables_jackknife.pl
> reading sources... [ 66%] csg/scripts/tag_file.sh
> reading sources... [ 67%] csg/scripts/update_ibi.sh
> reading sources... [ 67%] csg/scripts/update_ibi_pot.pl
> reading sources... [ 68%] csg/scripts/update_ibi_single.sh
> reading sources... [ 68%] csg/scripts/update_iie.sh
> reading sources... [ 69%] csg/scripts/update_imc.sh
> reading sources... [ 69%] csg/scripts/update_imc_single.sh
> reading sources... [ 70%] csg/scripts/update_optimizer.sh
> reading sources... [ 70%] csg/scripts/update_optimizer_single.sh
> reading sources... [ 71%] csg/scripts/update_re.sh
> reading sources... [ 71%] csg/theory
> reading sources... [ 71%] csg/topol
> reading sources... [ 72%] index
> reading sources... [ 72%] tools/index
> reading sources... [ 73%] tools/reference
> reading sources... [ 73%] tools/votca_compare
> reading sources... [ 74%] tools/votca_help2doc
> reading sources... [ 74%] tools/votca_property
> reading sources... [ 75%] websiteAndDocumentation
> reading sources... [ 75%] xtp-tutorials/DFTGWBSE_ENERGY
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> 0.00s - Debugger warning: It seems that frozen modules are being used, which may
> 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
> 0.00s - Debugger warning: It seems that frozen modules are being used, which may
> 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> reading sources... [ 76%] xtp-tutorials/DFTGWBSE_OPTIMIZATION
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> 0.00s - Debugger warning: It seems that frozen modules are being used, which may
> 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> reading sources... [ 76%] xtp-tutorials/LAMMPS_KMC
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> 0.00s - Debugger warning: It seems that frozen modules are being used, which may
> 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> reading sources... [ 77%] xtp-tutorials/QMMM_GROMACS
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> 0.00s - Debugger warning: It seems that frozen modules are being used, which may
> 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> reading sources... [ 77%] xtp-tutorials/QMMM_LAMMPS
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> 0.00s - Debugger warning: It seems that frozen modules are being used, which may
> 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
> /usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/sbuild-nonexistent' is not a writable location, using a temp directory.
>   warn("IPython parent '{0}' is not a writable location,"
> reading sources... [ 78%] xtp-tutorials/XTP-TUTORIAL
> reading sources... [ 78%] xtp-tutorials/help
> reading sources... [ 79%] xtp/Architecture
> reading sources... [ 79%] xtp/XTP-MANUAL
> reading sources... [ 80%] xtp/apdft
> reading sources... [ 80%] xtp/coupling
> reading sources... [ 81%] xtp/densityanalysis
> reading sources... [ 81%] xtp/dftgwbse
> reading sources... [ 82%] xtp/eanalyze
> reading sources... [ 82%] xtp/einternal
> reading sources... [ 83%] xtp/eqm
> reading sources... [ 83%] xtp/excitoncoupling
> reading sources... [ 84%] xtp/gencube
> reading sources... [ 84%] xtp/gpu_benchmark
> reading sources... [ 85%] xtp/ianalyze
> reading sources... [ 85%] xtp/iexcitoncl
> reading sources... [ 86%] xtp/iqm
> reading sources... [ 86%] xtp/kmclifetime
> reading sources... [ 86%] xtp/kmcmultiple
> reading sources... [ 87%] xtp/log2mps
> reading sources... [ 87%] xtp/mapchecker
> reading sources... [ 88%] xtp/mol2orb
> reading sources... [ 88%] xtp/molpol
> reading sources... [ 89%] xtp/neighborlist
> reading sources... [ 89%] xtp/orb2fchk
> reading sources... [ 90%] xtp/orb2mol
> reading sources... [ 90%] xtp/partialcharges
> reading sources... [ 91%] xtp/qmmm
> reading sources... [ 91%] xtp/reference
> reading sources... [ 92%] xtp/spectrum
> reading sources... [ 92%] xtp/theory
> reading sources... [ 93%] xtp/vaverage
> reading sources... [ 93%] xtp/workflows_and_calculators
> reading sources... [ 94%] xtp/xtp_autogen_mapping
> reading sources... [ 94%] xtp/xtp_basisset
> reading sources... [ 95%] xtp/xtp_introduction
> reading sources... [ 95%] xtp/xtp_map
> reading sources... [ 96%] xtp/xtp_map_overview
> reading sources... [ 96%] xtp/xtp_modify_jobfile
> reading sources... [ 97%] xtp/xtp_parallel
> reading sources... [ 97%] xtp/xtp_parallel_overview
> reading sources... [ 98%] xtp/xtp_qmmm2qm
> reading sources... [ 98%] xtp/xtp_run
> reading sources... [ 99%] xtp/xtp_run_overview
> reading sources... [ 99%] xtp/xtp_tools
> reading sources... [100%] xtp/xtp_tools_overview
> reading sources... [100%] xtp/xtp_update_mapfile
> 
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/xtp/Architecture.rst:3: WARNING: Duplicate explicit target name: "dftgwbse".
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/xtp/reference.rst:27: WARNING: Title underline too short.
> 
> xtp_modify_jobfile
> ^^^^^^^^^^^
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sphinx/xtp/reference.rst:27: WARNING: Title underline too short.
> 
> xtp_modify_jobfile
> ^^^^^^^^^^^
> looking for now-outdated files... none found
> pickling environment... done
> checking consistency... done
> preparing documents... done
> copying assets... copying static files... done
> copying extra files... done
> done
> writing output... [  0%] Architecture
> 
> Theme error:
> An error happened in rendering the page Architecture.
> Reason: UndefinedError("'style' is undefined")
> make[5]: *** [share/doc/CMakeFiles/doc.dir/build.make:81: share/doc/CMakeFiles/doc] Error 2


The full build log is available from:
http://qa-logs.debian.net/2023/07/30/exp/votca_2022.1-1_unstable_sphinx-exp.log

Please see [1] for Sphinx changelog and [2] for Docutils changelog.

Also see [3] for the list of deprecated/removed APIs in Sphinx and possible
alternatives to them.

Some notable changes in Sphinx 6 and Sphinx 7:

- Sphinx no longer includes jquery.js and underscore.js by default.
  Please use python3-sphinxcontrib.jquery package if you are using a custom
  template and it still needs jquery.

- The setup.py build_sphinx command was removed. Please instead call
  sphinx-build or "python3 -m sphinx" directly.

- For packages using the extlinks extension, the caption should contain
  exactly one "%s" placeholder (if caption is not None).

In case you have questions, please Cc sphinx at packages.debian.org on reply.

[1]: https://www.sphinx-doc.org/en/master/changes.html
[2]: https://repo.or.cz/docutils.git/blob/refs/tags/docutils-0.20.1:/RELEASE-NOTES.txt
[3]: https://www.sphinx-doc.org/en/master/extdev/deprecated.html#dev-deprecated-apis

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=sphinx7.1;users=python-modules-team@lists.alioth.debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=sphinx7.1&fusertaguser=python-modules-team@lists.alioth.debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects