Error when trying to build PDF file with user guide

[DariuszKamil]

The documentation of MDAnalyis is utilizing the Sphinx software, consist of ".rst" files, and contains both "conf.py" and "Makefile". It seems that all conditions to create a PDF file containing a user guide are fulfilled. A single PDF file is very useful for printing and when there is a need to work offline.

To create a single PDF file, I performed the following steps:

git clone https://github.com/MDAnalysis/UserGuide
cd UserGuide
conda env create --file environment.yml --quiet
conda activate mda-user-guide
cd doc
make latexpdf

The last command resulted in obtaining many warning and error messages:

$ make latexpdf
./source/scripts/generate_all.sh
/home/dboczar/miniconda3/envs/mda-user-guide/bin/python
2.11.0-dev0
2.11.0-dev0
Wrote  /home/dboczar/UserGuide/doc/source/formats/format_overview.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMAPP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMTOPOLOGY.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/GRO.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TPR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRZ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XPDB.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XTC.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/DMS.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/DCD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/DATA.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/NCDF.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TNG.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/GSD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPSDUMP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/ITP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/CONFIG.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TXYZ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/IN.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/GMS.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/INPCRD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TOP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XML.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PQR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/HISTORY.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/H5MD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDB.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/MMTF.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMSIMULATION.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRC.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/MOL2.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/COOR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XYZ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDBQT.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/RDKIT.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/CRD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PSF.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRJ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPS.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PARMED.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/CHEMFILES.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/IMD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/selection_exporter_formats.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/protein.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/protein_backbone.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/nucleic.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_backbone.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/base.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_sugar.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/groupmethods.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/defaults.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/topology_parsers.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/topologyattrs.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/connectivityattrs.txt
Wrote  generated/units_table.txt
Running Sphinx v9.1.0
/home/dboczar/miniconda3/envs/mda-user-guide/bin/python
2.11.0-dev0
2.11.0-dev0
Wrote  /home/dboczar/UserGuide/doc/source/formats/format_overview.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMAPP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMSIMULATION.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRC.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PARMED.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/IN.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/H5MD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/NCDF.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/INPCRD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/RDKIT.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PQR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/DCD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/CRD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/COOR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/GRO.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TOP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/HISTORY.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/DMS.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XYZ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPSDUMP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/MMTF.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/GMS.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRJ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMTOPOLOGY.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TPR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/ITP.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TXYZ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TNG.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/MOL2.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/CONFIG.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPS.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PSF.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDBQT.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/GSD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XPDB.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XML.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDB.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/CHEMFILES.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/DATA.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRZ.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/IMD.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/XTC.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRR.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/selection_exporter_formats.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/protein.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/protein_backbone.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/nucleic.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_backbone.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/base.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_sugar.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/groupmethods.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/defaults.txt
Wrote  /home/dboczar/UserGuide/doc/source/formats/topology_parsers.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/topologyattrs.txt
Wrote  /home/dboczar/UserGuide/doc/source/generated/topology/connectivityattrs.txt
Wrote  generated/units_table.txt
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/dboczar/UserGuide/doc/source/references.bib... parsed 35 entries
[autosummary] generating autosummary for: advanced_topology.rst, atomgroup.rst, contributing.rst, contributing_code.rst, contributing_docs.rst, datasets.rst, examples/README.rst, examples/analysis/README.rst, examples/analysis/alignment_and_rms/README.rst, examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb, ..., releases.md, selections.rst, standard_selections.rst, testing.rst, topology_system.rst, trajectories/slicing_trajectories.rst, trajectories/trajectories.rst, trajectories/transformations.rst, units.rst, universe.rst
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'mdanalysis' from https://docs.mdanalysis.org/2.11.0-dev0/objects.inv ...
loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest/objects.inv ...
loading intersphinx inventory 'chemfiles' from https://chemfiles.org/chemfiles.py/latest/objects.inv ...
loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ...
myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
building [mo]: targets for 0 po files that are out of date
writing output... 
building [latex]: all documents
updating environment: [new config] 116 added, 0 changed, 0 removed
reading sources... [ 20%] examples/analysis/distances_and_contacts/distances_between_atomgrreading sources... [ 21%] examples/analysis/distances_and_contacts/distances_between_selectreading sources... [ 22%] examples/analysis/distances_and_contacts/distances_within_selectireading sources... [ 37%] examples/analysis/trajectory_similarity/clustering_ensemble_similreading sources... [ 39%] examples/analysis/trajectory_similarity/dimension_reduction_ensemreading sources... [ 40%] examples/analysis/trajectory_similarity/harmonic_ensemble_similar/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/auxiliary/EDR.py:350: UserWarning: Could not find unit type for the following units: ['K', 'bar', '', 'nm^3', 'kg/m^3', 'bar nm']
  warnings.warn(
reading sources... [100%] universe
/home/dboczar/UserGuide/doc/source/contributing_code.rst:586: WARNING: Duplicate explicit target name: "black". [docutils]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:465: ERROR: Duplicate target name, cannot be used as a unique reference: "black". [docutils]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:465: ERROR: Duplicate target name, cannot be used as a unique reference: "black". [docutils]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:578: ERROR: Duplicate target name, cannot be used as a unique reference: "black". [docutils]
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/README.rst:7: WARNING: duplicate label alignment-and-rms, other instance in /home/dboczar/UserGuide/doc/source/examples/analysis/README.rst
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/README.rst:7: WARNING: duplicate label hydrogen-bonds, other instance in /home/dboczar/UserGuide/doc/source/examples/analysis/README.rst
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/README.rst:6: WARNING: duplicate label trajectory-similarity, other instance in /home/dboczar/UserGuide/doc/source/examples/analysis/README.rst
WARNING: 
>>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/formats/auxiliary.rst at block ending on line 282
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
<ipython-input-49-1eb00ff78cf2>:1: UserWarning: FigureCanvasAgg is non-interactive, and thus cannot be shown
  plt.show()
<<<-------------------------------------------------------------------------
/home/dboczar/UserGuide/doc/source/formats/coordinates.rst:4: WARNING: duplicate label coordinate-readers, other instance in /home/dboczar/UserGuide/doc/source/formats/coordinates.rst
WARNING: 
>>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 35
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:296: UserWarning: No coordinate reader found for /home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
  warnings.warn(
<<<-------------------------------------------------------------------------
WARNING: 
>>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 35
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:1940: UserWarning: This Universe has no coordinates
  warnings.warn(str(e))
<<<-------------------------------------------------------------------------
WARNING: 
>>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 53
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:296: UserWarning: No coordinate reader found for /home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
  warnings.warn(
<<<-------------------------------------------------------------------------
WARNING: 
>>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 77
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:296: UserWarning: No coordinate reader found for /home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
  warnings.warn(
<<<-------------------------------------------------------------------------
WARNING: 
>>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line None
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/coordinates/DCD.py:171: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
  warnings.warn("DCDReader currently makes independent timesteps"
<<<-------------------------------------------------------------------------
/home/dboczar/UserGuide/doc/source/preparing_releases_and_hotfixes.rst:214: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
WARNING: 
>>>-------------------------------------------------------------------------
Warning in <rst_epilogue> at block ending on line 1
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/coordinates/DCD.py:171: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
  warnings.warn("DCDReader currently makes independent timesteps"
<<<-------------------------------------------------------------------------
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/dboczar/UserGuide/doc/source/formats/guessers/default.rst: WARNING: document isn't included in any toctree [toc.not_included]
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/aligning_structure_to_another
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/aligning_trajectory
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/aligning_trajectory_to_frame.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/aligning_trajectory_to_frame
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/pairwise_rmsd
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/rmsd.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/rmsd
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/rmsf.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/rmsf
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_custom.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_custom
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_native_fraction.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_native_fraction
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_q1q2.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_q1q2
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_within_cutoff.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_within_cutoff
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/distances_between_atomgroups.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/distances_between_atomgroups
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/distances_between_selections.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/distances_between_selections
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/distances_within_selection.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/distances_within_selection
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/hbonds.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/hydrogen_bonds/README'], selecting: examples/analysis/hydrogen_bonds/README <- examples/analysis/hydrogen_bonds/hbonds
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/hbonds-lifetimes.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/hydrogen_bonds/README'], selecting: examples/analysis/hydrogen_bonds/README <- examples/analysis/hydrogen_bonds/hbonds-lifetimes
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/hbonds-selections.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/hydrogen_bonds/README'], selecting: examples/analysis/hydrogen_bonds/README <- examples/analysis/hydrogen_bonds/hbonds-selections
/home/dboczar/UserGuide/doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/polymers_and_membranes/README'], selecting: examples/analysis/polymers_and_membranes/README <- examples/analysis/polymers_and_membranes/hole2
/home/dboczar/UserGuide/doc/source/examples/analysis/polymers_and_membranes/polymer.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/polymers_and_membranes/README'], selecting: examples/analysis/polymers_and_membranes/README <- examples/analysis/polymers_and_membranes/polymer
/home/dboczar/UserGuide/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/reduced_dimensions/README'], selecting: examples/analysis/reduced_dimensions/README <- examples/analysis/reduced_dimensions/diffusion_map
/home/dboczar/UserGuide/doc/source/examples/analysis/reduced_dimensions/pca.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/reduced_dimensions/README'], selecting: examples/analysis/reduced_dimensions/README <- examples/analysis/reduced_dimensions/pca
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/average_rdf.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/average_rdf
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/dihedrals.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/dihedrals
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/elastic_network.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/elastic_network
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/helanal.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/helanal
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/site_specific_rdf.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/site_specific_rdf
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/clustering_ensemble_similarity.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/clustering_ensemble_similarity
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/convergence.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/convergence
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/harmonic_ensemble_similarity.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/harmonic_ensemble_similarity
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/psa.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/psa
/home/dboczar/UserGuide/doc/source/examples/analysis/volumetric/density_analysis.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/volumetric/README'], selecting: examples/analysis/volumetric/README <- examples/analysis/volumetric/density_analysis
/home/dboczar/UserGuide/doc/source/examples/analysis/volumetric/linear_density.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/volumetric/README'], selecting: examples/analysis/volumetric/README <- examples/analysis/volumetric/linear_density
/home/dboczar/UserGuide/doc/source/examples/quickstart.ipynb: document is referenced in multiple toctrees: ['examples/README', 'index'], selecting: index <- examples/quickstart
done
preparing documents... done
copying assets... 
copying TeX support files... Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/Makefile
Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/latexmkrc
Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/make.bat
Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/latexmkjarc
done
copying assets: done
processing mdanalysisuserguide.tex... 
index
 installation
 examples/quickstart
 faq
 examples/README
  examples/constructing_universe
  examples/transformations/README
   examples/transformations/center_protein_in_box
  examples/other/README
   examples/other/parmed_sim
   examples/analysis/alignment_and_rms/README
    examples/analysis/alignment_and_rms/aligning_structure_to_another
    examples/analysis/alignment_and_rms/aligning_trajectory
    examples/analysis/alignment_and_rms/aligning_trajectory_to_frame
    examples/analysis/alignment_and_rms/rmsd
    examples/analysis/alignment_and_rms/pairwise_rmsd
    examples/analysis/alignment_and_rms/rmsf
   examples/analysis/distances_and_contacts/README
    examples/analysis/distances_and_contacts/distances_between_atomgroups
    examples/analysis/distances_and_contacts/distances_between_selections
    examples/analysis/distances_and_contacts/distances_within_selection
     examples/analysis/distances_and_contacts/contacts_native_fraction
     examples/analysis/distances_and_contacts/contacts_q1q2
     examples/analysis/distances_and_contacts/contacts_within_cutoff
     examples/analysis/distances_and_contacts/contacts_custom
   examples/analysis/trajectory_similarity/README
    examples/analysis/trajectory_similarity/psa
    examples/analysis/trajectory_similarity/harmonic_ensemble_similarity
    examples/analysis/trajectory_similarity/clustering_ensemble_similarity
    examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity
    examples/analysis/trajectory_similarity/convergence
   examples/analysis/structure/README
    examples/analysis/structure/elastic_network
    examples/analysis/structure/average_rdf
    examples/analysis/structure/site_specific_rdf
    examples/analysis/structure/dihedrals
    examples/analysis/structure/helanal
   examples/analysis/reduced_dimensions/README
    examples/analysis/reduced_dimensions/pca
    examples/analysis/reduced_dimensions/diffusion_map
   examples/analysis/polymers_and_membranes/README
    examples/analysis/polymers_and_membranes/polymer
    examples/analysis/polymers_and_membranes/hole2
   examples/analysis/volumetric/README
    examples/analysis/volumetric/linear_density
    examples/analysis/volumetric/density_analysis
 releases
  universe
  atomgroup
  groups_of_atoms
  selections
  topology_system
  guessing
   trajectories/trajectories
   trajectories/slicing_trajectories
   trajectories/transformations
   units
    reading_and_writing
    formats/index
    formats/auxiliary
    formats/selection_exporters
    formats/format_reference
     formats/reference/chemfiles
     formats/reference/config
     formats/reference/coor
     formats/reference/crd
     formats/reference/data
     formats/reference/dcd
     formats/reference/dcd_lammps
     formats/reference/dms
     formats/reference/gms
     formats/reference/gro
     formats/reference/gsd
     formats/reference/in
     formats/reference/inpcrd
     formats/reference/itp
     formats/reference/lammpsdump
     formats/reference/mmtf
     formats/reference/mol2
     formats/reference/ncdf
     formats/reference/parmed
     formats/reference/pdb
     formats/reference/pdbqt
     formats/reference/pqr
     formats/reference/psf
     formats/reference/tng
     formats/reference/top
     formats/reference/tpr
     formats/reference/trj
     formats/reference/trr
     formats/reference/trz
     formats/reference/txyz
     formats/reference/xml
     formats/reference/xpdb
     formats/reference/xtc
     formats/reference/xyz
     examples/analysis/README
              examples/analysis/hydrogen_bonds/hbonds
              examples/analysis/hydrogen_bonds/hbonds-selections
              examples/analysis/hydrogen_bonds/hbonds-lifetimes
     examples/analysis/custom_trajectory_analysis
     examples/analysis/custom_parallel_analysis
      standard_selections
      advanced_topology
      datasets
       contributing
       contributing_code
       contributing_docs
       preparing_releases_and_hotfixes
       module_imports
       testing
       references

resolving references...
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:24: WARNING: undefined label: 'h5md-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:26: WARNING: undefined label: 'imd-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:38: WARNING: undefined label: 'openmmapp-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:39: WARNING: undefined label: 'openmmsimulation-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:40: WARNING: undefined label: 'openmmtopology-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:48: WARNING: undefined label: 'rdkit-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:53: WARNING: undefined label: 'trc-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:24: WARNING: undefined label: 'h5md-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:26: WARNING: undefined label: 'imd-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:37: WARNING: undefined label: 'openmmapp-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:38: WARNING: undefined label: 'openmmsimulation-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:43: WARNING: undefined label: 'rdkit-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:47: WARNING: undefined label: 'trc-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:719: WARNING: undefined label: 'travis' [ref.ref]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:719: WARNING: undefined label: 'appveyor' [ref.ref]
/home/dboczar/UserGuide/doc/source/testing.rst:108: WARNING: undefined label: 'appveyor' [ref.ref]
/home/dboczar/UserGuide/doc/source/testing.rst:110: WARNING: undefined label: 'travis' [ref.ref]
WARNING: Could not fetch remote image: https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true [429]
WARNING: Could not fetch remote image: https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true [404]
processing mdanalysisuserguide.tex: failed
sphinx-sitemap: No pages generated for sitemap.xml


Versions
========

* Platform:         linux; (Linux-6.14.0-37-generic-x86_64-with-glibc2.39)
* Python version:   3.12.13 (CPython)
* Sphinx version:   9.1.0
* Docutils version: 0.22.4
* Jinja2 version:   3.1.6
* Pygments version: 2.19.2

Last Messages
=============

           contributing_code
           contributing_docs
           preparing_releases_and_hotfixes
           module_imports
           testing
           references

    resolving references...
    processing mdanalysisuserguide.tex: failed
    sphinx-sitemap: No pages generated for sitemap.xml

Loaded Extensions
=================

* sphinx.ext.mathjax (9.1.0)
* alabaster (1.0.0)
* sphinxcontrib.applehelp (2.0.0)
* sphinxcontrib.devhelp (2.0.0)
* sphinxcontrib.htmlhelp (2.1.0)
* sphinxcontrib.serializinghtml (1.1.10)
* sphinxcontrib.qthelp (2.0.0)
* sphinx.ext.autodoc (9.1.0)
* sphinx.ext.autosummary (9.1.0)
* sphinx.ext.intersphinx (9.1.0)
* sphinx.ext.ifconfig (9.1.0)
* sphinx.ext.viewcode (9.1.0)
* sphinx.ext.napoleon (9.1.0)
* sphinx.ext.githubpages (9.1.0)
* sphinx_sitemap (2.9.0)
* nbsphinx (0.9.8)
* IPython.sphinxext.ipython_console_highlighting (unknown version)
* IPython.sphinxext.ipython_directive (unknown version)
* sphinxcontrib.bibtex (2.6.5)
* matplotlib.sphinxext.plot_directive (3.10.8)
* mdanalysis_sphinx_theme (1.3.1)
* myst_parser (5.0.0)

Traceback
=========

      File "/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/sphinx/builders/latex/transforms.py", line 487, in get_footnote_by_reference
        raise ValueError(__('No footnote was found for given reference node %r') % node)
    ValueError: No footnote was found for given reference node <footnote_reference: <#text: '1'>>


The full traceback has been saved in:
/tmp/sphinx-err-7vm4s53_.log

To report this error to the developers, please open an issue at <https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.
make: *** [Makefile:31: latexpdf] Error 1

Can I easily fix it?

[orbeckst]

Did you confirm that you can build the html docs successfully?

[DariuszKamil]

Dear @orbeckst, thank you for your interest.
I performed the following steps:

conda activate mda-user-guide
cd ~/UserGuide/doc
make clean
make html

and succeeded in building HTML documentation. Meanwhile, I obtained a lot of warnings in Terminal, many of them being similar as during the generation of a PDF file. As the Terminal output was much longer than previously, I enclose a text file containing it: mdanalysis-UserGuide.log

Meanwhile, I found out a previous attempt to build PDF in another issue (#136). The problems mentioned there referred to creating the table of contents properly.

I am also aware that MDAnalysis Documentation (https://docs.mdanalysis.org/stable/) and User Guide (https://userguide.mdanalysis.org/stable/) are two different issues and hence may require different treatment.

[orbeckst]

Thanks for trying the html build and confirming that it works.

I am not sure if anyone from the core team has the bandwidth to look into the PDF building issue as this is not something we have supported in the past. If this is important to you then I encourage you find a solution and contribute it to the project — we very much welcome all contributions, given that this is an open source project!